LMU BioDB 2013 - User contributions [en]

User:Dondi

2015-08-29T22:59:24Z

Dondi: Long-overdue typo fix.

:Associate Professor, [http://www.cs.lmu.edu Computer Science]
:Associate Director, [http://www.lmu.edu/honors University Honors Program]
:http://myweb.lmu.edu/dondi

== Education ==

=== May 1993 to December 1996 ===

University of California, Los Angeles

:Doctor of Philosophy, Computer Science
:Dissertation: ''An Integrated Data Model, Language, and User Interface for Knowledge, Multimedia, and Simulations''
:Major: Database and Knowledge Base Management
:Minors: Computer System Architecture, Scientific Computing

=== September 1991 to May 1993 ===

University of California, Los Angeles

:Master of Science, Computer Science
:Major: Database and Knowledge Base Management

=== September 1987 to May 1991 ===

Loyola Marymount University, Los Angeles

:Bachelor of Science, Summa cum Laude, Computer Science
:Minors: Music, Mathematics

== Selected Publications ==

[[Image:076378060X.jpg|right|link=http://www.jblearning.com/catalog/9780763780609/]]
[[Image:0763766585.jpg|right|link=http://www.jblearning.com/catalog/9780763766580/]]

Dionisio JDN, Burns WG, Gilbert R. “3D virtual worlds and the Metaverse: Current status and future possibilities.” ''ACM Computing Surveys'' '''45'''(3):1-38, June 2013. http://dl.acm.org/citation.cfm?id=2480741.2480751

Dionisio JDN, Toal R. ''Programming with JavaScript: Algorithms and Applications for Desktop and Mobile Browsers''. Jones and Bartlett Learning, 2013.

Toal R, Dionisio JDN. ''The JavaScript Programming Language''. Jones and Bartlett Publishers, 2009.

Dionisio JDN, Dahlquist KD. “Improving the computer science in bioinformatics through open source pedagogy.” ''ACM SIGCSE Bulletin'' '''40'''(2):115-119, June 2008. http://dl.acm.org/citation.cfm?id=1383602.1383648

Dionisio JDN, Dickson CL, August SE, Dorin PM, Toal R. “An open source software culture in the undergraduate computer science curriculum.” ''ACM SIGCSE Bulletin'' '''39'''(2):70-74, June 2007. http://dl.acm.org/citation.cfm?id=1272848.1272888

== Personal Interests ==

:Lego!

[[Image:TowerOfOrthanc.png]]

== Wiki Housekeeping ==

* Here is a page I created: [[Dondi Week 2]]
* My table of contents template: [[Template:Dondi]]

Here's my template in action:

{{Dondi}}

[[Dondi Week 9]]

[[Category:Individual Homework]]
[[Category:User Page]]

File:Bacterial infections and involved species.png

2014-02-01T19:14:21Z

Dondi: Test upload of .png file

Test upload of .png file

Week 15

2013-12-17T07:44:15Z

Dondi: (belatedly) Remove “Under Construction.”

'''This journal entry is due on Friday, December 6, at midnight PST.''' ''(Thursday night/Friday morning)''

== Individual Journal Assignment ==

* From this week on, your Individual Journal Assignment will be to complete your electronic laboratory notebook that records your work on your team's final project.
** You need to record a narrative that describes all of the methods that you are using in enough detail so that the instructors or your other team members can follow and reproduce your work.
** Include links to artifacts you produce (files, images, testing reports, code, etc.)
* Store this journal entry as "''username'' Week 12" (i.e., this is the text to place between the square brackets when you link to this page). Alternately, you may wish to keep your narrative for Weeks 12, 13, and 14 on the same page so that all of your work is in one place, in which case, you could name it something like "''username'' Project Notebook".
* Link to this journal entry from your user page.
* Link back from your journal entry to your user page.
* In addition, link your journal entry to your team's home page and vice versa.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
* Add your team's category to your wiki page as well.

== Team Journal Assignment ==

* As a group, create a status report as to progress on each milestone that that you have set for the week.
* Store your status report in a shared "''Teamname'' Week 15 Status Report" page.
* Link to your status report from your team's home page and vice versa.
* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
* Add the "Journal Entry" category and your team's category to the end of the wiki page.

=== Reflection ===

Each team member should reflect on the team's progress:
# What worked?
# What didn't work?
# What will I do next to fix what didn't work?

[[Category:Assignment]]
[[Category: Group Projects]]

Gene Database Project

2013-12-12T18:07:55Z

Dondi: /* Individual */ Add note about individual assessment delivery method.

== Deliverables ==

* You will give a final group PowerPoint presentation in class on '''Thursday, December 12, 8:00am'''.
* Final due date for all other deliverables is no later than '''Friday, December 13, 4:30pm''' (according to official final exam schedule for fall 2013)
* The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on CD to either Dr. Dahlquist or Dr. Dionisio.
* Each member of the group will be assigned the same grade for the group project.

=== Group ===
* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'')
* GenMAPP Expression Dataset file (''.gex'')
* Filtered MAPPFinder Results (''.xls'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Report Guidelines#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'' or ''.pdf'')
* PowerPoint presentation (''.ppt'', given on Thursday, December 12)

=== Individual ===
* [[Gene Database Project Report Guidelines#Individual Assessment and Reflection | Assessment and reflection]] on process (either wiki or email, depending on your preference; see note in the linked section)
** Statement of work
** Assessment of the work done
** What was learned
** Team evaluation via the [https://www.catme.org CATME] survey
**: ''You will, or should have already, received an email message from the CATME system with login instructions on your '''LMU email account''' (not necessarily the preferred email address that you listed in the wiki).''

== Team Journal Entries ==

* Each team will write a combined journal entry for each week with contributions from all members.
* [[Week 10]] Creation of page (midnight 11/1)
* [[Week 11]] (midnight 11/7)
* [[Week 12]] (midnight 11/15)
* [[Week 13]] (midnight 11/22)
* [[Week 15]] (midnight 12/6)

== Groups ==

The project groups are:
# Team 1
#* Coder: Katrina
#* Quality Assurance: Hilda
#* GenMAPP User: Dillon
# Team 2
#* Coder: Tauras
#* Quality Assurance: Alina
#* GenMAPP User: Kevin Meilek
# Team 3
#* Coder: Gabriel
#* Quality Assurance: Lena
#* GenMAPP Users: Kevin McGee and Viktoria
# Team 4
#* Coder: Mitchell
#* Quality Assurance: Stephen
#* GenMAPP Users: Lauren and Miles

=== Roles (Guilds) ===

As the project moves forward, we will use class time for team meetings. In addition, we will also have guild meetings where students sharing the same role can work together on common issues. Each student has been assigned a primary role in the project by the instructors. 

==== [[Project Manager]] (PM) ====

The project manager makes sure that individuals are fulfilling their roles and performing the tasks on time.

==== [[GenMAPP User]] (GU) ====

The GenMAPP user runs GenMAPP with the microarray dataset (Expression Dataset Manager, MAPPFinder, GenMAPP MAPP).

==== [[Quality Assurance]] (QA) ====

The Quality Assurance team member is the resident expert on species ID systems and formats. He or she should be proficient with ''XMLPipeDB Match'', SQL queries in PostgreSQL, and Microsoft Access to navigate through the data and find missing IDs, discrepancies, sanity checks, etc.

==== [[Coder]] (C) ====

The coder is the resident expert on the technology being used — assorted software, file management, some troubleshooting, possibly some programming. He or she coordinates with Drs. Dahlquist and Dionisio in extending GenMAPP Builder code and making new versions

== Project Milestones ==

Specific project milestones are found on the individual guild pages.

=== Overall Flow ===

A successful project will have the following steps from end to end. Depending on the data and/or other issues that are encountered, one or more of these steps may go through iterations, repetitions, or refinements.

[[Image:ProjectWorkflow.jpg|450px|thumb|right|Overall Flow]]

# Following the steps shown in the [[Running GenMAPP Builder]] instructions, download the UniProt XML proteome set and GOA (GO association) files for your species.
#* Make sure that you are choosing the correct strain/subspecies as the microarray data you have.
#* Note the date of download and the version of the file on your Gene Database Testing Report.
# Download GO terms from [http://beta.geneontology.org/page/download-ontology Gene Ontology].
#* You will need the OBO-XML format, the "obo-xml.gz" file.
#* Note the date of download and the version of the file on your Gene Database Testing Report.
# Create the GenMAPP Builder tables in PostgreSQL.
# Load files into PostgreSQL database via GenMAPP Builder.
# Export into a GenMAPP Gene Database.
# Inspect/vet/validate Gene Database.
#* Create a [[Gene Database Testing Report Sample | Gene Database Testing Report]] each time a new export is run.
#* Compare to the model organism database for your species
# Find an original journal article describing a DNA microarray experiment performed on your species.
#* Download the microarray data for this article.
#* Consult with Dr. Dahlquist about the proper steps to take to process the data (normalization, statistical analysis) and perform the analysis
# Run GenMAPP using the Gene Database.
#* Microarray data (import using Expression Dataset Manager)
#* MAPPFinder
#* Place genes on MAPP and draw pathway

=== Guild Milestones ===

These are links to the respective milestone lists in the guild pages.

* [[Project Manager#Milestones|Project Manager]]
* [[GenMAPP User#Milestones|GenMAPP User]]
* [[Quality Assurance#Milestones|Quality Assurance]]
* [[Coder#Milestones|Coder]]

[[Category:Group Projects]]

Gene Database Project Report Guidelines

2013-12-12T18:06:24Z

Dondi: /* Individual Assessment and Reflection */ Add clarification on assessment and reflection.

== Group Report ==

* The report should be written with contributions from all group members.
* Submit as ''.doc'' or ''.pdf'' file.

=== Style Sheet ===

Use the following guidelines when formatting your report.
* 1" margins
* double-spaced
* Times New Roman, 12 point font
* Number the pages
* Title page should include a descriptive title for your project, the names of the team members, the course number and title of the class, and the date of submission

=== Introduction ===

The introduction gives the background information necessary to understand your report. The introduction should be in the form of a logical argument that "funnels" from broad to narrow:

[[Image:Funnel.jpg]]
* States importance of the problem
Why is this species important?
* States what is known about the problem
Give an overview of what is known about your species' genome from your [[Week 11 | journal club outline and presentation]].
Introduce the DNA microarray experiment that was performed on your species.
* States what is unknown about the problem
You want to analyze the data with GenMAPP/MAPPFinder, but can't because there is no Gene Database for your species
* States clues that suggest how to approach the unknown
Introduce XMLPipeDB and GenMAPP Builder as the answer to this problem
* States the question the paper is trying to address
In this case you want to discover new information about the microarray data using GenMAPP

=== Methods ===

* This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did.
# Download the UniProt XML proteome set and GOA (GO association) files for your species.
#* Note the date of download and the version of the files.
# Download GO terms from in the OBO-XML format.
#* Note the date of download and the version of the files.
# Create the GenMAPP Builder tables in PostgreSQL.
# Load files into PostgreSQL database via GenMAPP Builder.
# Export into a GenMAPP Gene Database.
# Inspect/vet/validate Gene Database.
# Prepare microarray data (organize, normalize, perform statistical analysis)
# Run GenMAPP using the Gene Database.
#* Microarray data (import using Expression Dataset Manager)
#* Run MAPPFinder analysis
#* Place genes on MAPP and draw pathway

=== Results ===

* This section will summarize the results of the project. This section will include figures, tables, and '''''narrative description''''' of the results shown in those figures and tables. You should include:
** Gene Database Schema
** Gene Database Testing Report on final version of Gene Database
** Report on quantity and identity of gene IDs that did not make it into the database
**# Gene IDs that were not in the XML source at all
**# Gene IDs that were in the XML source but did not get imported into Postgres
**# Gene IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
** Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs
*** If your team was able to make such changes, report on the results of these changes
** Report results of the DNA microarray analysis
*** How many genes were significantly increased and decreased in the dataset? (including your criteria for a significant increase or decrease)
*** Table of MAPPFinder results (from .xls)
*** GenMAPP MAPP of a pathway relevant to your results

=== Discussion ===

* How well did the GenMAPP Builder process work for your species (just comment on the technical aspects here, you will discuss the teamwork/process aspects in your individual assessment).
* Discuss the statistical analysis and MAPPFinder results for your microarray dataset. Compare it to what was reported in the original paper from which you got the microarray data.

=== References ===

* Please use the [[Guidelines for Literature Citations in a Scientific Paper]]. The [http://en.wikipedia.org/wiki/APA_style#Citation APA format] is also very similar to these guidelines and will be acceptable. Be consistent with your format for the in text citations and for your references list at the end.

=== Acknowledgments ===

* (Optional): Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

== Individual Assessment and Reflection ==

* Each person on the team will complete an assessment and reflection ''individually''. If you are comfortable with making this assessment publicly available, you may write it up as a wiki page. If you prefer to communicate your assessment privately, then email this to both Drs. Dahlquist and Dionisio.

=== Statement of Work ===

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
* What worked and what didn't work?
* What would you do differently if you could do it all over again?
* Evaluate the Gene Database Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

[[Category:Group Projects]]

Main Page

2013-12-12T15:52:53Z

Dondi: /* Course Assessment */ Add CATME under course assessment.

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Course Assessment ===

* We ask that students in this class participate in the [http://www.grinnell.edu/academic/psychology/faculty/dl/risc/ Research on the Integrated Science Curriculum (RISC) Survey] which will allow the instructors to evaluate the effectiveness of this course. Please complete the [https://survey.grinnell.edu/se.ashx?s=251137453158E327 student post-course survey] using "Dahlquist" as the instructor last name.

* Please note also that as part of the deliverables, we ask that you fill out the confidential team evaluation [https://www.catme.org CATME] survey
*: ''You will, or should have already, received an email message from the CATME system with login instructions on your '''LMU email account''' (not necessarily the preferred email address that you listed in the wiki).''

=== Downloading and Installing GenMAPP and MAPPFinder ===

* If you want to install GenMAPP and MAPPFinder on your own computer to use over the break, the instructions can be found on the [[Week_8#Downloading_and_installing_the_GenMAPP_and_MAPPFinder_Software | Week 8 Assignment]] page. Note that this software is Windows-only.

=== Grades Posted ===

* Grades for the [[Week 10]] Team pages have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based was discussed in class on Tuesday, November 5.

* Grades for the [[Week 11]] presentation have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based was distributed during the December 3 class, one set per group.

* Grades for the [[Week 9]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based can be found in your user discussion pages.

* Grades for the [[Week 7]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. Be sure to pick up your hard copy of the graded assignment on Thursday, December 12.

=== Seminars and Events ===

* '''Chemistry Department Seminar:''' Friday, December 6, 2:00 PM S200, Dr. Joel Ornelas, Resident physician in diagnostic radiology at the Los Angeles County University of Southern California (LAC+USC) Medical Center and the Keck Medical Center of USC, ''Inorganic Chemistry and Physics in the Practice of Modern Medicine''
** To receive extra credit for attending this seminar, turn in a one-page reflection to Dr. Dahlquist on what you learned by Friday, December 13.

=== Class Locations ===

* Final presentations on Thursday, December 12 will take place in the ''classroom''.

== Group Projects ==

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

=== Teams ===

{| style="width: 75%"
| '''[[Chlamydia trachomatis | Team H(oo)KD]]'''
| '''[[Streptococcus pneumoniae | Team ATK]]'''
| '''[[Leishmania major | Off The Leish]]'''
| [[[[Team Name]]]]
|}

=== Guilds ===

{| style="width: 75%"
| [[Project Manager]]
| [[Coder]]
| [[Quality Assurance]]
| [[GenMAPP User]]
|}

=== Undergraduate Library Research Award ===

The projects for this course will qualify for the Hannon Library’s [http://digitalcommons.lmu.edu/ulra/ Undergraduate Library Research Award (ULRA)]. Click on the link if you are interested in this competition.


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 75%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
|
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma
* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Moody (2004) Chapter 6 (on MyLMU Connect]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]

[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]

| style="vertical-align: top; background: #eee" |Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class (MyLMU Connect)]
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

| style="vertical-align: top" | Introduction to relational databases
* Case study from one of the NAR databases: http://www.rhesusbase.org 
* Relating XML structure to relational structure

Test your understanding: http://xkcd.com/327/
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27 and 10/1)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations part 1
# Hilda - Mitchell
# Kurt - Kevin Meilak
# Tauras - Miles - Lena
# Lauren - Dillon

[[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Database presentations part 2
# Viktoria - Kevin McGee
# Katrina - Gabriel
# Stephen - Alina

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Campbell & Heyer Chapter 4 (on MyLMU Connect)]

| style="vertical-align: top" | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]

| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" | [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]

Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger et al. (2003) "MAPPFinder"
''Genome Biology'']]
| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Work session to complete DNA Microarray Analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']

[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
| style="vertical-align: top; background: #eee" |
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
* Groups assigned and species chosen
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guest speaker: Librarian Glenn Johnson-Grau
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Annotated bibliography of genomics papers for your species
** Select genome paper for journal club
** Select microarray paper
| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/12)

''Note different due date''

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

Gene Database Project

2013-12-11T19:52:48Z

Dondi: /* Individual */ Add CATME information.

== Deliverables ==

* You will give a final group PowerPoint presentation in class on '''Thursday, December 12, 8:00am'''.
* Final due date for all other deliverables is no later than '''Friday, December 13, 4:30pm''' (according to official final exam schedule for fall 2013)
* The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on CD to either Dr. Dahlquist or Dr. Dionisio.
* Each member of the group will be assigned the same grade for the group project.

=== Group ===
* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'')
* GenMAPP Expression Dataset file (''.gex'')
* Filtered MAPPFinder Results (''.xls'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Report Guidelines#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'' or ''.pdf'')
* PowerPoint presentation (''.ppt'', given on Thursday, December 12)

=== Individual ===
* [[Gene Database Project Report Guidelines#Individual Assessment and Reflection | Assessment and reflection]] on process
** Statement of work
** Assessment of the work done
** What was learned
** Team evaluation via the [https://www.catme.org CATME] survey
**: ''You will, or should have already, received an email message from the CATME system with login instructions on your '''LMU email account''' (not necessarily the preferred email address that you listed in the wiki).''

== Team Journal Entries ==

* Each team will write a combined journal entry for each week with contributions from all members.
* [[Week 10]] Creation of page (midnight 11/1)
* [[Week 11]] (midnight 11/7)
* [[Week 12]] (midnight 11/15)
* [[Week 13]] (midnight 11/22)
* [[Week 15]] (midnight 12/6)

== Groups ==

The project groups are:
# Team 1
#* Coder: Katrina
#* Quality Assurance: Hilda
#* GenMAPP User: Dillon
# Team 2
#* Coder: Tauras
#* Quality Assurance: Alina
#* GenMAPP User: Kevin Meilek
# Team 3
#* Coder: Gabriel
#* Quality Assurance: Lena
#* GenMAPP Users: Kevin McGee and Viktoria
# Team 4
#* Coder: Mitchell
#* Quality Assurance: Stephen
#* GenMAPP Users: Lauren and Miles

=== Roles (Guilds) ===

As the project moves forward, we will use class time for team meetings. In addition, we will also have guild meetings where students sharing the same role can work together on common issues. Each student has been assigned a primary role in the project by the instructors. 

==== [[Project Manager]] (PM) ====

The project manager makes sure that individuals are fulfilling their roles and performing the tasks on time.

==== [[GenMAPP User]] (GU) ====

The GenMAPP user runs GenMAPP with the microarray dataset (Expression Dataset Manager, MAPPFinder, GenMAPP MAPP).

==== [[Quality Assurance]] (QA) ====

The Quality Assurance team member is the resident expert on species ID systems and formats. He or she should be proficient with ''XMLPipeDB Match'', SQL queries in PostgreSQL, and Microsoft Access to navigate through the data and find missing IDs, discrepancies, sanity checks, etc.

==== [[Coder]] (C) ====

The coder is the resident expert on the technology being used — assorted software, file management, some troubleshooting, possibly some programming. He or she coordinates with Drs. Dahlquist and Dionisio in extending GenMAPP Builder code and making new versions

== Project Milestones ==

Specific project milestones are found on the individual guild pages.

=== Overall Flow ===

A successful project will have the following steps from end to end. Depending on the data and/or other issues that are encountered, one or more of these steps may go through iterations, repetitions, or refinements.

[[Image:ProjectWorkflow.jpg|450px|thumb|right|Overall Flow]]

# Following the steps shown in the [[Running GenMAPP Builder]] instructions, download the UniProt XML proteome set and GOA (GO association) files for your species.
#* Make sure that you are choosing the correct strain/subspecies as the microarray data you have.
#* Note the date of download and the version of the file on your Gene Database Testing Report.
# Download GO terms from [http://beta.geneontology.org/page/download-ontology Gene Ontology].
#* You will need the OBO-XML format, the "obo-xml.gz" file.
#* Note the date of download and the version of the file on your Gene Database Testing Report.
# Create the GenMAPP Builder tables in PostgreSQL.
# Load files into PostgreSQL database via GenMAPP Builder.
# Export into a GenMAPP Gene Database.
# Inspect/vet/validate Gene Database.
#* Create a [[Gene Database Testing Report Sample | Gene Database Testing Report]] each time a new export is run.
#* Compare to the model organism database for your species
# Find an original journal article describing a DNA microarray experiment performed on your species.
#* Download the microarray data for this article.
#* Consult with Dr. Dahlquist about the proper steps to take to process the data (normalization, statistical analysis) and perform the analysis
# Run GenMAPP using the Gene Database.
#* Microarray data (import using Expression Dataset Manager)
#* MAPPFinder
#* Place genes on MAPP and draw pathway

=== Guild Milestones ===

These are links to the respective milestone lists in the guild pages.

* [[Project Manager#Milestones|Project Manager]]
* [[GenMAPP User#Milestones|GenMAPP User]]
* [[Quality Assurance#Milestones|Quality Assurance]]
* [[Coder#Milestones|Coder]]

[[Category:Group Projects]]

Main Page

2013-12-05T17:53:09Z

Dondi: /* Announcements */ Add course post-assessment link.

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Course Assessment ===

We ask that students in this class participate in the [http://www.grinnell.edu/academic/psychology/faculty/dl/risc/ Research on the Integrated Science Curriculum (RISC) Survey] which will allow the instructors to evaluate the effectiveness of this course. Please complete the [https://survey.grinnell.edu/se.ashx?s=251137453158E327 student post-course survey] using "Dahlquist" as the instructor last name.

=== Downloading and Installing GenMAPP and MAPPFinder ===

* If you want to install GenMAPP and MAPPFinder on your own computer to use over the break, the instructions can be found on the [[Week_8#Downloading_and_installing_the_GenMAPP_and_MAPPFinder_Software | Week 8 Assignment]] page. Note that this software is Windows-only.

=== Grades Posted ===

* Grades for the [[Week 11]] presentation have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based was distributed during the December 3 class, one set per group.

* Grades for the [[Week 9]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based can be found in your user discussion pages.

* Grades for the [[Week 7]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. Hard copies of the corrected questions will be handed out in class on Tuesday, November 12.

=== Seminars and Events ===

=== Class Locations ===

* We will meet in ''lab'' for the remainder of the semester.
* Final presentations on Thursday, December 12 will take place in the ''classroom''.

== Group Projects ==

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

=== Teams ===

{| style="width: 75%"
| '''[[Chlamydia trachomatis | Team H(oo)KD]]'''
| '''[[Streptococcus pneumoniae | Team ATK]]'''
| '''[[Leishmania major | Off The Leish]]'''
| [[[[Team Name]]]]
|}

=== Guilds ===

{| style="width: 75%"
| [[Project Manager]]
| [[Coder]]
| [[Quality Assurance]]
| [[GenMAPP User]]
|}

=== Undergraduate Library Research Award ===

The projects for this course will qualify for the Hannon Library’s [http://digitalcommons.lmu.edu/ulra/ Undergraduate Library Research Award (ULRA)]. Click on the link if you are interested in this competition.


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 75%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
|
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma
* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Moody (2004) Chapter 6 (on MyLMU Connect]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]

[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]

| style="vertical-align: top; background: #eee" |Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class (MyLMU Connect)]
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

| style="vertical-align: top" | Introduction to relational databases
* Case study from one of the NAR databases: http://www.rhesusbase.org 
* Relating XML structure to relational structure

Test your understanding: http://xkcd.com/327/
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27 and 10/1)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations part 1
# Hilda - Mitchell
# Kurt - Kevin Meilak
# Tauras - Miles - Lena
# Lauren - Dillon

[[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Database presentations part 2
# Viktoria - Kevin McGee
# Katrina - Gabriel
# Stephen - Alina

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Campbell & Heyer Chapter 4 (on MyLMU Connect)]

| style="vertical-align: top" | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]

| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" | [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]

Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger et al. (2003) "MAPPFinder"
''Genome Biology'']]
| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Work session to complete DNA Microarray Analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']

[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
| style="vertical-align: top; background: #eee" |
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
* Groups assigned and species chosen
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guest speaker: Librarian Glenn Johnson-Grau
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Annotated bibliography of genomics papers for your species
** Select genome paper for journal club
** Select microarray paper
| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/12)

''Note different due date''

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

Gene Database Project

2013-12-05T08:23:04Z

Dondi: /* Individual */ Add CATME survey note.

== Deliverables ==

* You will give a final group PowerPoint presentation in class on '''Thursday, December 12, 8:00am'''.
* Final due date for all other deliverables is no later than '''Friday, December 13, 4:30pm''' (according to official final exam schedule for fall 2013)
* The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on CD to either Dr. Dahlquist or Dr. Dionisio.
* Each member of the group will be assigned the same grade for the group project.

=== Group ===
* GenMAPP Gene Database for assigned species (''.gdb'')
* ReadMe file to accompany the Gene Database (''.pdf'')
** Sample ReadMe in Word format: [[Media:ReadMe_Vc-Std_External_20131122.zip | ReadMe_Vc-Std_External_20131122.zip]]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'')
* GenMAPP Expression Dataset file (''.gex'')
* Filtered MAPPFinder Results (''.xls'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Report Guidelines#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'' or ''.pdf'')
* PowerPoint presentation (''.ppt'', given on Thursday, December 12)

=== Individual ===
* [[Gene Database Project Report Guidelines#Individual Assessment and Reflection | Assessment and reflection]] on process
** Statement of work
** Assessment of the work done
** What was learned
** Team evaluation via the [https://www.catme.org CATME] survey (instructions to be posted next week)

== Team Journal Entries ==

* Each team will write a combined journal entry for each week with contributions from all members.
* [[Week 10]] Creation of page (midnight 11/1)
* [[Week 11]] (midnight 11/7)
* [[Week 12]] (midnight 11/15)
* [[Week 13]] (midnight 11/22)
* [[Week 15]] (midnight 12/6)

== Groups ==

The project groups are:
# Team 1
#* Coder: Katrina
#* Quality Assurance: Hilda
#* GenMAPP User: Dillon
# Team 2
#* Coder: Tauras
#* Quality Assurance: Alina
#* GenMAPP User: Kevin Meilek
# Team 3
#* Coder: Gabriel
#* Quality Assurance: Lena
#* GenMAPP Users: Kevin McGee and Viktoria
# Team 4
#* Coder: Mitchell
#* Quality Assurance: Stephen
#* GenMAPP Users: Lauren and Miles

=== Roles (Guilds) ===

As the project moves forward, we will use class time for team meetings. In addition, we will also have guild meetings where students sharing the same role can work together on common issues. Each student has been assigned a primary role in the project by the instructors. 

==== [[Project Manager]] (PM) ====

The project manager makes sure that individuals are fulfilling their roles and performing the tasks on time.

==== [[GenMAPP User]] (GU) ====

The GenMAPP user runs GenMAPP with the microarray dataset (Expression Dataset Manager, MAPPFinder, GenMAPP MAPP).

==== [[Quality Assurance]] (QA) ====

The Quality Assurance team member is the resident expert on species ID systems and formats. He or she should be proficient with ''XMLPipeDB Match'', SQL queries in PostgreSQL, and Microsoft Access to navigate through the data and find missing IDs, discrepancies, sanity checks, etc.

==== [[Coder]] (C) ====

The coder is the resident expert on the technology being used — assorted software, file management, some troubleshooting, possibly some programming. He or she coordinates with Drs. Dahlquist and Dionisio in extending GenMAPP Builder code and making new versions

== Project Milestones ==

Specific project milestones are found on the individual guild pages.

=== Overall Flow ===

A successful project will have the following steps from end to end. Depending on the data and/or other issues that are encountered, one or more of these steps may go through iterations, repetitions, or refinements.

[[Image:ProjectWorkflow.jpg|450px|thumb|right|Overall Flow]]

# Following the steps shown in the [[Running GenMAPP Builder]] instructions, download the UniProt XML proteome set and GOA (GO association) files for your species.
#* Make sure that you are choosing the correct strain/subspecies as the microarray data you have.
#* Note the date of download and the version of the file on your Gene Database Testing Report.
# Download GO terms from [http://beta.geneontology.org/page/download-ontology Gene Ontology].
#* You will need the OBO-XML format, the "obo-xml.gz" file.
#* Note the date of download and the version of the file on your Gene Database Testing Report.
# Create the GenMAPP Builder tables in PostgreSQL.
# Load files into PostgreSQL database via GenMAPP Builder.
# Export into a GenMAPP Gene Database.
# Inspect/vet/validate Gene Database.
#* Create a [[Gene Database Testing Report Sample | Gene Database Testing Report]] each time a new export is run.
#* Compare to the model organism database for your species
# Find an original journal article describing a DNA microarray experiment performed on your species.
#* Download the microarray data for this article.
#* Consult with Dr. Dahlquist about the proper steps to take to process the data (normalization, statistical analysis) and perform the analysis
# Run GenMAPP using the Gene Database.
#* Microarray data (import using Expression Dataset Manager)
#* MAPPFinder
#* Place genes on MAPP and draw pathway

=== Guild Milestones ===

These are links to the respective milestone lists in the guild pages.

* [[Project Manager#Milestones|Project Manager]]
* [[GenMAPP User#Milestones|GenMAPP User]]
* [[Quality Assurance#Milestones|Quality Assurance]]
* [[Coder#Milestones|Coder]]

[[Category:Group Projects]]

Main Page

2013-12-03T19:41:17Z

Dondi: /* Grades Posted */ Add week 11 notice.

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Downloading and Installing GenMAPP and MAPPFinder ===

* If you want to install GenMAPP and MAPPFinder on your own computer to use over the break, the instructions can be found on the [[Week_8#Downloading_and_installing_the_GenMAPP_and_MAPPFinder_Software | Week 8 Assignment]] page. Note that this software is Windows-only.

=== Grades Posted ===

* Grades for the [[Week 11]] presentation have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based was distributed during the December 3 class, one set per group.

* Grades for the [[Week 9]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based can be found in your user discussion pages.

* Grades for the [[Week 7]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. Hard copies of the corrected questions will be handed out in class on Tuesday, November 12.

=== Seminars and Events ===

=== Class Locations ===

* We will meet in ''lab'' for the remainder of the semester.
* Final presentations on Thursday, December 12 will take place in the ''classroom''.

== Group Projects ==

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

=== Teams ===

{| style="width: 75%"
| '''[[Chlamydia trachomatis | Team H(oo)KD]]'''
| '''[[Streptococcus pneumoniae | Team ATK]]'''
| '''[[Leishmania major | Off The Leish]]'''
| [[[[Team Name]]]]
|}

=== Guilds ===

{| style="width: 75%"
| [[Project Manager]]
| [[Coder]]
| [[Quality Assurance]]
| [[GenMAPP User]]
|}

=== Undergraduate Library Research Award ===

The projects for this course will qualify for the Hannon Library’s [http://digitalcommons.lmu.edu/ulra/ Undergraduate Library Research Award (ULRA)]. Click on the link if you are interested in this competition.


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 75%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
|
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma
* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Moody (2004) Chapter 6 (on MyLMU Connect]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]

[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]

| style="vertical-align: top; background: #eee" |Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class (MyLMU Connect)]
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

| style="vertical-align: top" | Introduction to relational databases
* Case study from one of the NAR databases: http://www.rhesusbase.org 
* Relating XML structure to relational structure

Test your understanding: http://xkcd.com/327/
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27 and 10/1)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations part 1
# Hilda - Mitchell
# Kurt - Kevin Meilak
# Tauras - Miles - Lena
# Lauren - Dillon

[[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Database presentations part 2
# Viktoria - Kevin McGee
# Katrina - Gabriel
# Stephen - Alina

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Campbell & Heyer Chapter 4 (on MyLMU Connect)]

| style="vertical-align: top" | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]

| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" | [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]

Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger et al. (2003) "MAPPFinder"
''Genome Biology'']]
| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Work session to complete DNA Microarray Analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']

[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
| style="vertical-align: top; background: #eee" |
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
* Groups assigned and species chosen
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guest speaker: Librarian Glenn Johnson-Grau
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Annotated bibliography of genomics papers for your species
** Select genome paper for journal club
** Select microarray paper
| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/12)

''Note different due date''

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

Main Page

2013-11-30T00:53:21Z

Dondi: /* Grades Posted */ Announce week 9 grade postings.

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Downloading and Installing GenMAPP and MAPPFinder ===

* If you want to install GenMAPP and MAPPFinder on your own computer to use over the break, the instructions can be found on the [[Week_8#Downloading_and_installing_the_GenMAPP_and_MAPPFinder_Software | Week 8 Assignment]] page. Note that this software is Windows-only.

=== Grades Posted ===

* Grades for the [[Week 9]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. The feedback on which the grades are based can be found in your user discussion pages.

* Grades for the [[Week 7]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. Hard copies of the corrected questions will be handed out in class on Tuesday, November 12.

=== Seminars and Events ===

=== Class Locations ===

* We will meet in ''lab'' for the remainder of the semester.
* Final presentations on Thursday, December 12 will take place in the ''classroom''.

== Group Projects ==

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

=== Teams ===

{| style="width: 75%"
| '''[[Chlamydia trachomatis | Team H(oo)KD]]'''
| '''[[Streptococcus pneumoniae | Team ATK]]'''
| '''[[Leishmania major | Off The Leish]]'''
| [[[[Team Name]]]]
|}

=== Guilds ===

{| style="width: 75%"
| [[Project Manager]]
| [[Coder]]
| [[Quality Assurance]]
| [[GenMAPP User]]
|}

=== Undergraduate Library Research Award ===

The projects for this course will qualify for the Hannon Library’s [http://digitalcommons.lmu.edu/ulra/ Undergraduate Library Research Award (ULRA)]. Click on the link if you are interested in this competition.


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 75%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
|
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma
* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Moody (2004) Chapter 6 (on MyLMU Connect]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]

[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]

| style="vertical-align: top; background: #eee" |Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class (MyLMU Connect)]
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

| style="vertical-align: top" | Introduction to relational databases
* Case study from one of the NAR databases: http://www.rhesusbase.org 
* Relating XML structure to relational structure

Test your understanding: http://xkcd.com/327/
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27 and 10/1)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations part 1
# Hilda - Mitchell
# Kurt - Kevin Meilak
# Tauras - Miles - Lena
# Lauren - Dillon

[[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Database presentations part 2
# Viktoria - Kevin McGee
# Katrina - Gabriel
# Stephen - Alina

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Campbell & Heyer Chapter 4 (on MyLMU Connect)]

| style="vertical-align: top" | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]

| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" | [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]

Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger et al. (2003) "MAPPFinder"
''Genome Biology'']]
| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Work session to complete DNA Microarray Analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']

[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
| style="vertical-align: top; background: #eee" |
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
* Groups assigned and species chosen
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guest speaker: Librarian Glenn Johnson-Grau
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Annotated bibliography of genomics papers for your species
** Select genome paper for journal club
** Select microarray paper
| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/12)

''Note different due date''

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

User talk:Dwilliams

2013-11-30T00:44:18Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You noted that there were problems with your .gdb file to the wiki, but by all accounts this was most likely a transient problem, and there is no indication that you went back and tried to upload the file again.
* You successfully ran the Tally Engine.
* You appear to have successfully run xmlpipedb-match, but reported only the results without posting primary documentation of this activity (e.g., screenshots, exact numeric output).
* There is no indication that you successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access, but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You do not note differences and similarities in the ID tallies from your various counts, particularly the large ''OrderedLocusNames'' discrepancy between your .gdb file and the benchmark version.
* There is no indication of the ID pattern(s) used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for the link from your journal entry page back to your user page and inclusion of the ''Journal Entry'' category.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:44, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* It was difficult for me to find your Week 8 files for review. While you uploaded them to the wiki, you did not link to them from any pages.
* Once I did find them and download I saw that you need to add a date to the filename to follow the file naming convention requested in the assignment. For example, my filename could be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls".
* Otherwise, the calculations you performed are correct and you are ready to go for Tuesday's exercise.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:14, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You missed quite a few wiki skills and requested information. For the wiki skills, consult the list below. For the requested information, if the answer to a question is nothing (e.g., independent research), then explicitly say "none" or "n/a" so that we know it wasn't forgotten.

'''Items for completion/follow-up:'''
* Snail mail address
* Upper-division courses (you mentioned not taking them in your email, but have not stated this on the wiki)
* Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
* Work experience—again, if you haven’t had such experience, just say “n/a” or “none” so that we know you haven’t forgotten this.
* Change summaries—enter these more consistently.
* Create a new wiki page
* Link to a page within the wiki
* Link to an external site
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Assign a category to a wiki page
* Create and use a template
* Link to an assignment (Week ''n'') page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:59, 3 September 2013 (PDT)

I answered your question on my user [[User talk:Kdahlquist | talk]] page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:09, 5 September 2013 (PDT)''

=== Week 1 Follow-up Feedback ===

Thank you for filling in some of the missing information/wiki skills from last week. You have some leftover items, and we encourage you to continue filling those out beyond this assignment—you will find that the practice will only make things easier going forward. Here’s the updated list of what we haven’t seen you do yet. (I left in the ones missing last week, but did them in strikeout style so you can see your progress better)

* Snail mail address
* Upper-division courses (you mentioned not taking them in your email, but have not stated this on the wiki)
* Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
* Work experience—again, if you haven’t had such experience, just say “n/a” or “none” so that we know you haven’t forgotten this.
* <del>Change summaries—enter these more consistently.</del> ''—Your more recent changes all have summaries; by all means maintain that habit.''
* <del>Create a new wiki page</del>
* <del>Link to a page within the wiki</del>
* Link to an external site
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* <del>Assign a category to a wiki page</del>
* Create and use a template
* Link to an assignment (Week ''n'') page ''—You will find that, as assignments accumulate and grow in depth, it will be useful to have links within reach for going back and referring to them; that is why we are specifically asking for this.''

Keep up the wiki practice!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:49, 8 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time.
* Your translation of all six frames was incorrect. There was probably a mistake in the sequence or it was translated in the wrong direction. Please use the ExPaSY tool to translate it and figure out where you went wrong. You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections listed below. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* You are missing several links requested in the assignment:
*# You did not link from your user page to the shared class journal page.
*# You did not link from your user page to the [[Week 3]] Assignment page.
*# You did not link from your individual journal entry back to your user page.
*# You need to add the category "Journal Entry" to your individual week 2 journal entry page. We are not actually using the category "Individual Homework" like Dr. Dionisio demo'd in class; we apologize for any confustion this caused.
** If you add these four items to your template and then use your template on every journal entry, then you don't have to worry about forgetting them for subsequent assignments.
* The Nirenberg article was written as a memoir to other practicing biochemists. Hopefully, even though it was dense, you found learning about the process interesting.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:21, 11 September 2013 (PDT)''

=== Week 2 Follow-up ===

* I have reviewed the Week 2 assignment again and saw that you did not make any further changes to this page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:01, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Your experience with “Where’s my stuff” typically occurs when a computing system is strongly protecting file extensions like ''.txt'' and ''.html''. Different operating systems apply protections differently. Typically, there is a setting one can hit that tells the computer that you know what you are doing with respect to these extensions, after which you will then have greater control over these. In any case, nothing to worry about; what matters is that you got a sense for what role these file extensions play.
* Your '''sed''' and '''match''' skills are great! All of your commands were correct.
* You were missing a number of requested links and wiki elements:
** Your user page was missing a link to the shared journal page
** Your user page was also missing a link to the [[Week 3]] assignment page
** Your journal answer page was missing a link back to your user page
** Your journal answer page was also missing the requested ''Journal Entry'' category
:Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:50, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''The transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon was correctly identified with an appropriate command.
* ''You missed that the terminator includes 4 additional base pairs after the hairpin.''
* ''The mRNA strand is short—only the start-to-stop codon was identified, but transcription actually goes from the transcription start site to the end of the terminator.''
* You determined the correct amino acid sequence with an appropriate command.
In terms of your wiki link routine, your pages were missing the following:
* Link from user page to shared journal page.
* Correct page name for individual assignment page. (i.e., the name of the page was incorrect)
* Link from user page to [[Week 4]] assignment page.
* Link from individual assignment page to user page.

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:35, 24 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* I did not see an entry in the [[Class_Journal_Week_5 | Week 5 shared class reflection.]]
* On your individual Week 5 page, I did not see any evidence that you kept an electronic lab notebook recording your work on the UniProt exercise. Starting again with the [[Week 8]] assignment and for the rest of the semester, this will be an important component of your weekly assignment. Please let me know if you are unclear as to what this entails.
* You are also missing the link from your user page to the assignment page and the category on your journal entry. Looking at the feedback from past assignments, you seem to be consistently missing these. At this point in the semester using your template for these links should be routine. Again, please let me or Dr. Dionisio know if you need assistance with how to do this.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:43, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* This assignment is incomplete; I did not find a wiki page for GeneDB, am I missing something? ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:01, 11 October 2013 (PDT)''

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The 8th query and the last, individual query joins the ''member'' table, but that table is not actually necessary. When working with databases, we are sensitive to doing more work than necessary, because sometimes this additional work strongly detracts from speed, particularly if the tables contain large numbers of rows. An extra but unnecessary join will also, in some cases, change the results that you get back.
* In the last query as well, the plain English statement seeks only ratings of 3, but the SQL does not reflect this criterion.
* All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, these items were missing or not to-spec:
* Missing link from user page to shared journal page
* Missing link from user page to [[Week 6]] assignment page
* Missing “Journal Entry” category on your journal page
These requested links and features make the navigation of your wiki work as easy as possible, so please make a habit of this.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 12:35, 12 October 2013 (PDT)

User talk:Ajvree

2013-11-30T00:38:10Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You report one number for your xmlpipedb-match result, but do not provide details such as the text pattern(s) used or any commentary on the number you got vs. expected counts.
The following requested tasks were not accomplished (or, if you did do them, there is no record on the journal page that you did):
* Run the Tally Engine.
* Run the appropriate PostgreSQL query.
* Examine your .gdb file in Microsoft Access and compare the data against the benchmark version of the ''V. cholerae'' gene database.
* Note differences and similarities in the ID tallies from your various counts.
* Clearly indicate the ID pattern used for your ID searches/tallies.
* Lab notebook-style documentation of your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:38, 29 November 2013 (PST)

== Week 8 Feedback ==

* I have reviewed your .xls and .txt files from part 1 of the Week 8 assignment. They are correct and ready to go for Tuesday. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:28, 14 October 2013 (PDT)''
* Also, please follow the convention for naming your files given in the assignment. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". Your filename needs to have a date included. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:43, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You missed quite a few wiki skills and requested information, plus need to send email concerns. If the answer to a question is nothing (e.g., independent research), then explicitly say "none" or "n/a" so that we know it wasn't forgotten.

'''Items for completion/follow-up:'''
* Snail mail address
* Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
* Email about worries/concerns/questions/anything else
* Create a new wiki page
* Link to another page within the wiki (other than your user page)
* Link to an external site
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a (non-image) file
* Create and use a template
* Link to an assignment (Week ''n'') page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:51, 3 September 2013 (PDT)

=== Week 1 Follow-up Feedback ===

Thank you for filling in the missing information/wiki skills from last week. You have some leftover items, and we encourage you to continue filling those out beyond this assignment—you will find that the practice will only make things easier going forward. Here’s the updated list of what we haven’t seen you do yet. (I left in the ones missing last week, but did them in strikeout style so you can see your progress better)

* Snail mail address
* <del>Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.</del>
* <del>Email about worries/concerns/questions/anything else</del>
* <del>Create a new wiki page</del>
* <del>Link to a page within the wiki</del>
* <del>Link to an external site</del>
* Comments inside the wiki markup
* <del>Upload and link to an image</del>
* Upload and link to a (non-image) file
* <del>Create and use a template</del>
* <del>Link to an assignment (Week ''n'') page</del>

So, that’s a good number of things down. Keep up the wiki practice!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:41, 8 September 2013 (PDT)

== Week 2 Feedback ==

* Your translation of the genetic code was entirely correct. However, you submitted your assignment late. In the future, please make sure that you give yourself enough time to complete the assignment and submit it on time.
* You should remove the "Shared" category from your user page. We are reserving that category for pages with multiple authors, like the Class Journal pages.
* The Nirenberg article was written as a memoir to other practicing biochemists, so it was a bit dense. I'm glad that you enjoyed learning about the process, even if the article itself was tedious.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:15, 11 September 2013 (PDT)''

P.S. I answered your question on my user talk page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:20, 12 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:59, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Good to hear that you succeeded in exerting control of your file extensions.
* You missed supplying an answer for complementing a nucleotide sequence. I combed your notes at the top of the journal answer page and could not find it.
* Your '''sed''' and '''match''' skills are otherwise great! All of your commands were correct, except that the ''-F genetic-code.sed'' segments of your commands should have had a ''lowercase'' '''f'''. This is not a huge deal, but remember how attention to detail is a very important part of working with computers—if someone who did not know '''sed''' tried to type your answers verbatim on the command line, they would get an error.
* Regarding the '''match''' question comparing it to '''grep'''/'''wc''', in the third subquestion, the distinction we were looking for is the way '''grep'''/'''wc''' can only count lines, thus missing cases where a pattern appears more than once in a single line.
* Your journal page was missing the requested ''Journal Entry'' category. Again falling under the “attention to detail” heading, please note the bulleted checklist provided under the assignment headings.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:48, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was off by four bases.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* ''The stop codon was not correctly identified because the given command does not enforce base triplets after the start codon.''
* ''The terminator sequence is missing its end tag.''
* ''The mRNA strand is short—only the start-to-stop codon was identified, but transcription actually goes from the transcription start site to the end of the terminator.''
* ''The identified amino acid sequence is short due to the misidentified stop codon.''
In terms of your wiki link routine, everything was there except for:
* The specified category designation for your individual assignment page.
Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:32, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* The missing ''Journal Entry'' category in your Week 3 journal answer page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:34, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Your individual journal entry (UniProt Exercise) was submitted late.
* Your electronic lab notebook did not contain enough detail such that you or another person could reproduce what you did using only the information from your journal entry. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Look at some of your classmates' entries to see some examples and please let us know if you have any questions.
* Remember to link your journal page back to your user page and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:49, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Thank you for submitting your assignment on time. From the history, it looks like you were the main contributor to this page.
* You could have been more specific as to which species were covered in the database.
* OrganelleDB is not an example of a community database, a community database is basically like this wiki where a distributed set of users enters information directly into the database. Instead, OrganelleDB is an example of a specialty database.
* You could have provided more information about the sample query you tried.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:08, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* In your movies-beginning-with-the-word-“Star” query, you miss adding a space at the end of the ''"^Star"'' pattern—this matches more rows than desired, because without the space, your query will also get movies whose titles start with the words “Stare,” “Startle,” “Stark,” or “Start,” to name a few.
* The 8th query, which requests for counts by rating, is missing the ''group by'' clause. Thus, you needed to manually tally up the number of movies that got each individual rating. This was manageable for the small data set, but becomes unwieldy with large ones.
* A query of your own was not supplied (10th query).
* All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, a couple of items were missing:
* Link from the journal page back to your user page
* “Journal Entry” category on your journal page
These requested links and features make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 12:28, 12 October 2013 (PDT)

User talk:Taur.vil

2013-11-30T00:34:01Z

Dondi: Add week 9 feedback.

User talk:Ksherbina

2013-11-30T00:29:55Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are listed. The GO OBO information is missing; as indicated in the export report template, this should be the date/time stamp shown in the file properties after it has been unzipped.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:29, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I have reviewed your files from part 1 of Week 8. They are correct and ready to go for Tuesday.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:17, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Excellent coverage! (save for creating a new distinct wiki page) Plus, don't forget to email us your concerns and questions.

'''Items for completion/follow-up:'''
* Email about worries/concerns/questions/anything else
* Create a new wiki page (beyond your own user page)

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:45, 3 September 2013 (PDT)

* I have answered your question on my [[User talk:Kdahlquist|talk]] page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:36, 4 September 2013 (PDT)''

=== Week 1 Follow-Up Feedback ===

Thank you for sending is the questions/concerns email, and for creating a new wiki page. Moving right along then ''':)'''

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:13, 8 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time.
* As was discussed in class, you just had one missing amino acid in the -1 frame. For our purposes in this exercise, an open reading frame is simply one without a stop codon.
* Please go ahead and make these corrections on your page to earn back the points you missed.
* The Nirenberg article was written as a memoir to other practicing biochemists, so it was dense. I hope you enjoyed it anyway!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:08, 11 September 2013 (PDT)''

P.S. I answered your question on my user talk page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:19, 12 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:59, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Good to hear that you succeeded in exerting control of your file extensions.
* Your '''sed''' and '''match''' skills are great! All of your commands were correct.
* For the third '''match''' question, you missed that the command was supposed to have run on the ''hs_ref_GRCh37_chr19.fa'' file, not ''493.P_falciparum.xml''. The commands were still successful and you made the correct inference about how '''match''' and '''grep'''/'''wc''' are different, but you were using different data from what was specified.
* Thank you for providing a complete set of links across your user page, assignment page, shared journal page, and individual journal answer page. These really help us to get around from one page to another. The tabular arrangement makes things easy to spot as well.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:34, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''The transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon was correctly identified with an appropriate command.
* ''You missed that the terminator includes 4 additional base pairs after the hairpin.''
* ''The mRNA strand is short—only the start-to-stop codon was identified, but transcription actually goes from the transcription start site to the end of the terminator.''
* You determined the correct amino acid sequence with an appropriate command.
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:16, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a prior assignment:
* Your Week 4 wiki comments now have the correct code for locating the transcription start site.
* Your Week 4 wiki comments now have the correct code for marking up the complete terminator signal.
* Your Week 4 wiki comments now have the correct code for computing the complete mRNA strand. The revised command skips the substitution of '''t''' for '''u''', but because this was in the original command, the correction is interpreted as needing to address only the proper start and end of transcription.
:Regarding your question about why '''1,3D''' did not work as expected, note here that “1,3” represents an ''inclusive range''—i.e., lines 1 ''to'' 3. I understand how the comma threw you off—in many other systems, the comma indicates individual choice. In '''sed''', however, it indicates a range.

If you have any further questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:19, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was neat and complete. It could have been enhanced with hyperlinks to the actual pages that you visited (take advantage of the capabilities of a wiki!) as well as by some screenshots.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:57, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your database wiki page was complete and thorough, although it looks like some final tweaks were completed after the deadline. It appears that both of you contributed equally to the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:11, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* The 5th and 8th queries, which request counts by certain categories (year in the 5th query; rating in the 8th), require a ''group by'' clause in order to deliver the answers with maximum efficiency. Your answer to the 5th query returns the overall count for that decade, not the year-by-year tally; your answer to the 8th query involves 5 separate retrievals, where the use of ''group by'' would reduce that to a single one.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:28, 11 October 2013 (PDT)

User talk:Mpetredi

2013-11-30T00:26:39Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged relevant import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for the link from your individual journal entry page back to your user page.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:26, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I have checked your .xls and .txt files and they are correct and ready for tomorrow's exercise. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:02, 14 October 2013 (PDT)''
* Also, please follow the convention for naming your files given in the assignment. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". Your filename needs to have a date included and should have the extraneous hyphen removed. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:41, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Good coverage—make sure to fill out the links in your template, plus include missing requested information like snail mail address and upper division courses. Try to make your wiki change summaries a consistent habit. Also, don’t forget your email of concerns/questions.

'''Items for completion/follow-up:'''
* Snail mail address
* Upper-division courses—if you haven’t taken any, still say so explicitly, so that we know you didn’t forget about it.
* Email about worries/concerns/questions/anything else
* Change summaries—you did some, but ideally should have a summary for every change.
* Create a new wiki page
* Link to an assignment (Week ''n'') page
* Link ''to'' the shared journal ''from'' your user page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:42, 3 September 2013 (PDT)

=== Week 1 Follow-up Feedback ===

Thank you very much for completing the missing information/wiki skills from last week. You’ve improved your wiki summary consistency and have demonstrated all of the basic capabilities now. I just have some constructive comments about a couple of things:

* Some of your links (e.g., your links to the assignments) are actually internal to the wiki and are more succinctly linked with the double-bracket notation, not the single-bracket one that you used where you have to specify the full address (i.e., ''...xmlpipedb.cs.lmu.edu...''). When a page is wiki-internal, use '''[[''' ''']]''' instead.
* You copied your shared journal answers to separate pages—I’m not sure why you decided to do this. Was it because you wanted to have a direct link? You can still do that in the shared page—if you mouse over your name in the table of contents, the wiki adds a special suffix (beginning with ''#'') that provides a direct link to your entry. You can use that to send the browser directly to your entry. Let me know if this is what you were trying to do.

Good job rounding this out and keep it up!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:10, 8 September 2013 (PDT)

== Week 2 Feedback ==

* Your Week 2 journal entry was submitted on time and completely correct. Congratulations and keep up the good work!
* The Nirenberg article was written as a memoir to other practicing biochemists, so it is dense. I'm glad that you got a sense of how tough the experiments were. All of what is in textbooks currently was laboriously worked out by someone doing lots of experiments! :)

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:05, 11 September 2013 (PDT)''

P.S. I answered your question on my user talk page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:18, 12 September 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Good to hear that you succeeded in exerting control of your file extensions.
* Your '''sed''' and '''match''' skills are great with the exception of your 3'-5' +2 and +3 reading frame commands—you were eliminating the “skipped” bases ''before'' reversing the string and not after.
* For the first '''match''' question, you missed writing down your speculative answer on what that ''GO:...'' pattern may represent.
* You were missing a number of requested links and wiki elements:
** Your user page was missing a link to the shared journal page
** Your user page was also missing a link to the [[Week 3]] assignment page
:Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:31, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was incorrectly identified.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* ''The given stop codon command did not enforce triplets after the start codon.''
* The terminator signal was correctly identified ''but the given command makes assumptions about exactly how long the terminator is, requiring a priori knowledge that was not part of the consensus information''.
* ''The mRNA strand is incorrect—it is '''not''' the entire sequence, and it is complemented when it should not be.''
* The correct amino acid sequence was identified ''but the command that computed it was not provided''.
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:14, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* The missing link from your user page to the Week 3 shared journal page has been added.
* The missing link from your user page to the Week 3 assignment page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:07, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was neat and complete. Moving forward starting with the [[Week 8]] assignment, this will be an important part of each weekly assignment. Keep in mind the guideline that you or someone else should be able to reproduce what you did using only the information on your journal entry page. Your page could have been enhanced by showing one or more screenshots from your database exploration.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:00, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, it appears that you were the main contributor to this page.
* I see that you used a template to move this page content to one with the proper name. There is a better way to move pages, see the drop down arrow next to the "View history" tab at the top of the page.
* Be careful about the formatting of your hyperlinks. Only use two square brackets when linking to internal wiki pages; external links use only single square brackets. Also, the numbering of your page with respect to the questions is off.
* You could have elaborated a bit more on your answers to the questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:22, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:50, 11 October 2013 (PDT)

User talk:Kmeilak

2013-11-30T00:20:34Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access and compared its data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:20, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I have reviewed your files from part 1 of Week 8. They are correct and ready to go for Tuesday. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:10, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You show decent coverage of wiki skills, with just a few items missed. Your external file should be referenced using Media: instead of an external link (i.e., let the wiki do as much work for you as possible). Also, don’t forget your email of concerns/questions.

'''Items for completion/follow-up:'''
* Email about worries/concerns/questions/anything else
* Create a new wiki page 
* Link to an external site
* Comments inside the wiki markup
* Link ''to'' the shared journal ''from'' your user page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:38, 3 September 2013 (PDT)

I answered your question on my user [[User talk:Kdahlquist | talk]] page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 5 September 2013 (PDT)''

=== Week 1 Follow-up Feedback ===

Thank you for completing all of the items from last week! You’ve demonstrated the full set of basics now. I have some very minor comments:

* When doing an external link, the separator between the address and the text that you want the link to have is a space, not a vertical bar (|). That is why your LinkedIn page does not show the intended label. Replace that vertical bar with a space and the link will appear as you intended (I presume)
* Your direct link to your section of the shared journal is a good idea, but you didn’t have the correct label after the #. You have “#Kevin” there, when it should be “#Kevin_Meilak.” (you can tell because when you mouse over your name on the table of contents, that is what shows up after the # in the link address.

Good job! Keep it up.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:29, 8 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* As we discussed in class, your translation of all six frames was incorrect. There was probably a mistake in the sequence or it was translated in the wrong direction. Please use the ExPaSY tool to translate it and figure out where you went wrong. As was noted in class, you have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections listed below. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* You did not link from your individual journal entry back to your user page.
* You did not put the category "Journal Entry" on your individual journal page.
** If you add these to your template and then use your template on every journal entry, then you don't have to worry about forgetting them for subsequent assignments.
* The Nirenberg article was written as a memoir for other practicing biochemists, so it was dense to novices. Hopefully, it was still a good read.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:03, 11 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:58, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Your '''sed''' and '''match''' skills are great! All of your commands were correct.
* For the '''match''' questions, you did not provide speculative answers on what the search patterns could represent.
* Your user page was missing a link to the [[Class Journal Week 3]] page. Strongly consider using a template for this, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon ''sequence'' was correctly identified, ''but the supplied command does not indicate its location''.
* The terminator sequence was correctly identified ''but the command used to identify it makes more assumptions than were given in the consensus information''.
* The mRNA strand matches the range given by the transcription start site and the terminator ''but it was complemented when it should not have been''.
* ''The amino acid sequence was incorrect, and no command was given to show where the computation might have gone wrong.''
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:56, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* The missing link from your user page to the Week 3 shared journal page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:05, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was neat and complete. Moving forward starting with the [[Week 8]] assignment, this will be an important part of each weekly assignment. Keep in mind the guideline that you or someone else should be able to reproduce what you did using only the information on your journal entry page. Your page could have been enhanced by showing one or more screenshots from your database exploration.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:01, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* This assignment is complete and on time.
* You are missing a link from your user page to the Spliceosome Database wiki page you created. You are using your template well to provide all of the other links, don't forget to add this one.
* The assignment asked for links to all pages from which you answered the questions, not just one link to the main page of the database.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:05, 11 October 2013 (PDT)''

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* In your movies-beginning-with-the-word-“Star” query, you miss adding a space before the '''%''' in your ''"Star%"'' pattern—this matches more rows than desired, because without the space, your query will also get movies whose titles start with the words “Stare,” “Startle,” “Stark,” or “Start,” to name a few.
* Your last, individual query joins the ''member'' table, but that table is not actually necessary. When working with databases, we are sensitive to doing more work than necessary, because sometimes this additional work strongly detracts from speed, particularly if the tables contain large numbers of rows. An extra but unnecessary join will also, in some cases, change the results that you get back.
* The 8th query, which requests for counts by rating, is missing the ''group by'' clause. Thus, you needed to manually tally up the number of movies that got each individual rating. This was manageable for the small data set, but becomes unwieldy with large ones.
* The 9th query, which seeks the average rating for movies beginning with the word “Star,” has the same issue as the 4th query.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 12:16, 12 October 2013 (PDT)

User talk:Kevinmcgee

2013-11-30T00:16:15Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:16, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I have reviewed your spreadsheet from part 1 of the Week 8 assignment. Your made some errors on the "scaled_centered" sheet that have propagated through to the other sheets.
** When you calculated the AVERAGE and STDEV for each column, you used a comma instead of a colon to specify the cell range. The way you wrote it, it simply averages or computes the standard deviation of just those two values.
** When scaling and centering the log fold changes based on those values, you forgot the second dollar sign in the formula.
** The rest of your calculations are correct, but based on erroneous numbers from the previous sheet.
** You will need to correct your file or alternately work with your partner's file, if it is correct.
* The syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of <nowiki>[[File:filename]] use [[Media:filename]].</nowiki>

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:06, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You missed quite a few wiki skills, plus need to send email concerns and ask talk page questions.

'''Items for completion/follow-up:'''
* Snail mail address
* Expected graduation year
* Upper-division courses—if you haven’t taken any, still say so explicitly, so that we know you didn’t forget about it.
* Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
* Email about worries/concerns/questions/anything else
* Questions to faculty Talk pages
* Create a new wiki page
* Link to an external site
* Create a numbered list
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Assign a category to a page
* Use the signature shortcut
* Create and use a template
* Link to an assignment (Week ''n'') page
* Link ''to'' the shared journal ''from'' your user page
* Link ''from'' the shared journal ''to'' your user page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:35, 3 September 2013 (PDT)

=== Week 1 Follow-up Feedback ===

Thank you very much for catching up on last week’s missing information/wiki skills! You’ve now shown that you can do all of the basics. Please don’t forget to send Dr. Dahlquist and me an email listing your questions and concerns (and say “none” if you have none, just so that we know you didn’t forget).

Some very minor notes on your catch-up work:

* Now that you have made “Loyola Marymount University” a link, the text above it has become redundant and can be removed.
* In linking to your résumé, you use the ''File:'' wiki markup, which is fine but takes you to one more intermediate page before the user can actually see the file. If you precede the filename with ''Media:'' instead, then you will get a direct link which goes right to the document when the user clicks on it.

Congratulations and keep it up!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:22, 8 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* As was discussed in class, there were several mutations in your translation. Make sure you use the ExPaSY tool to translate the code and explain what went wrong with your translation.
* You forgot to put the category "Journal Entry" on your individual entry page.
** If you add the category to your template and then use your template every time in the future, you won't need to worry about forgetting it.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the correction above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* Yes, the Nirenberg article was dense. It was written as a memoir for other practicing biochemists. I'm glad you were able to grasp the big picture.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:54, 11 September 2013 (PDT)''

P.S. I answered your question on my user talk page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:15, 12 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making the corrections to your translation. You are still missing the first amino acid from frame "-2".
* The category is still missing from this page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:04, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* You missed the '''cat''' command at the beginning of your reading frame answers. This is not a huge deal, but remember how attention to detail is a very important part of working with computers.
* Your '''sed''' and '''match''' skills are otherwise great! All of your commands were correct.
* Thank you for providing a complete set of links across your user page, assignment page, shared journal page, and individual journal answer page. These really help us to get around from one page to another.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:21, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Transcription start site was not identified.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* ''Stop codon was not correctly identified because the command did not enforce solely triplets after the start codon.''
* ''The terminator is missing the complete hairpin sequence.''
* ''The identified mRNA strand is short—you only returned the start-to-stop codon, but transcription actually goes from the transcription start site to the end of the terminator. In addition, it appears that this sequence was derived manually.''
* ''The identified amino acid sequence is short, and no command was supplied so it is not clear where the computation went wrong.''
In terms of your wiki link routine, everything was there except for:
* The specified category designation for your individual assignment page.
Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:50, 24 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook did not contain enough detail such that you or another person could reproduce what you did using only the information from your journal entry. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Look at some of your classmates' entries to see some examples and please let us know if you have any questions.
* Remember to link your journal page back to your user page and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:04, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, it looks like you were the main contributor to this page.
* You need to link from the database wiki page to the [[Class Journal Week 5]] page.
* The main classification for Ensembl is that it is a sequence/ genome database.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:15, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]). Still, no answer was provided; note the instructions stated that you should provide a subset of the answers in the event that the total result was too long.
* The 5th query, which requests counts by year, is much easier to answer if you include ''year'' in the ''select'' clause. What you have still produces the right answer, but you have to be careful in determining which count pertains to which year. In particular, what if there was a year with zero movies? That might be missed in the tallies.
* In the 9th query, which requests the average rating for movies beginning with “Star,” you computed the average ''year'' and not the ''rating''.
* All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, a couple of items were missing:
* Link from the journal page back to your user page
* “Journal Entry” category on your journal page
These requested links and features make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 12:08, 12 October 2013 (PDT)

User talk:Mmalefyt

2013-11-30T00:12:43Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
The following requested tasks were not accomplished (or, if you did do them, there is no record on the journal page that you did):
* Run the Tally Engine.
* Run xmlpipedb-match.
* Run the appropriate PostgreSQL query.
* Examine your .gdb file in Microsoft Access and compare the data against the benchmark version of the ''V. cholerae'' gene database.
* Note differences and similarities in the ID tallies from your various counts.
* Clearly indicate the ID pattern used for your ID searches/tallies.
* Lab notebook-style documentation of your activities and results for this assignment.

Your work was submitted on time; however, the following specified wiki links and navigational aids were incorrect or missing:
* Correct page name for your individual journal page
* Link from your journal entry page back to your user page
* Inclusion of the ''Journal Entry'' category.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:12, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I have reviewed the content of your files from part 1 and they are correct and good to go for Tuesday.
* However, please follow the convention for naming your files given in the assignment, so that it is maximally informative as to the contents. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". You need to add a date to your filename. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:53, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You missed quite a few wiki skills, plus need to post to shared journal, send email concerns, and ask talk page questions. You started nicely with entering wiki change summaries, but petered out with your later changes. Strive to do your summaries consistently.

'''Items for completion/follow-up:'''
* Snail mail address
* Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
* Email about worries/concerns/questions/anything else
* Questions to faculty Talk pages
* Change summaries—enter these consistently.
* Create a new wiki page
* Link to a page within the wiki
* Link to an external site
* Create a numbered list
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Use the signature shortcut
* Create and use a template
* Link to an assignment (Week ''n'') page
* Link ''to'' the shared journal ''from'' your user page
* Link ''from'' the shared journal ''to'' your user page
* Place your signature in the shared journal page
* Answer questions on the readings in the shared journal

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:10, 3 September 2013 (PDT)

=== Week 1 Follow-up Feedback ===

Thank you for filling in some of the missing information/wiki skills from last week. You have some leftover items, and we encourage you to continue filling those out beyond this assignment—you will find that the practice will only make things easier going forward. Here’s the updated list of what we haven’t seen you do yet. (I left in the ones missing last week, but did them in strikeout style so you can see your progress better)

* Snail mail address
* Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
* Email about worries/concerns/questions/anything else
* Questions to faculty Talk pages
* Change summaries—you have gotten better with this but still have occasional gaps.
* <del>Create a new wiki page</del>
* <del>Link to a page within the wiki</del>
* <del>Link to an external site</del>
* <del>Create a numbered list</del>
* Comments inside the wiki markup
* <del>Upload and link to an image</del>
* Upload and link to a file
* <del>Use the signature shortcut</del> (in the shared journal page—kind of a double-dip; the other signature should be in your questions on our Talk pages)
* Create and use a template
* Link to an assignment (Week ''n'') page
* <del>Link ''to'' the shared journal ''from'' your user page</del>
* <del>Link ''from'' the shared journal ''to'' your user page</del>
* <del>Place your signature in the shared journal page</del>
* <del>Answer questions on the readings in the shared journal</del>

So, that’s a good number of things down. Keep up the wiki practice!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:14, 8 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* As was discussed in class, you had several "mutations" in your translations. You also needed to state which were the open reading frames (without stop codons). Make sure you go to the ExPaSY site to translate your sequence and explain what went wrong.
* You will need to work on completing/correcting the links requested as part of the assignment. Specifically:
*# We have a specific naming convention that we would like you to use when naming your new individual journal pages. You should name them ''username week #''; for example your week 2 assignment page should be named ''Mmalefyt Week 2'', instead of "Genetic Code". You will need to '''''move''''' the contents of your "Genetic Code" page to a page called "Mmalefyt Week 2". To do so, follow the directions listed [http://en.wikipedia.org/wiki/How_to_move_a_page here]]. We will be happy to talk you through this in class or office hours if you like. For the future, please make sure you are using the preferred naming convention for new pages.
*# You are missing the link from your User page to the [[Week 2 | Week 2 Assignment]] page.
*# You are missing the link from your individual week 2 journal entry back to your User page.
*# You are missing the link from your user page to the Class Journal Week 2 page.
*# You need to add the category "Journal Entry" to your individual week 2 journal entry page.
*#* For the four items above, you can add these links to your template and then just use your template on your user page and all journal entry pages. That way, you won't forget to put the links in future assignments.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections requested above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* When Moody was calling the four bases a binary code, he was saying that they could be expressed in binary, not that there were just two. To specify four different bases you would just use:
00
01
10
11

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:47, 11 September 2013 (PDT)''

P.S. I answered your question on my user talk page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:14, 12 September 2013 (PDT)''

=== Week 2 Follow-up ===

* I have reviewed the Week 2 assignment again and saw that you did not make any further changes to this page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:00, 11 October 2013 (PDT)''

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified ''but no command was supplied''.
* -10 box was correctly identified ''but no command was supplied''.
* Transcription start site was correctly identified ''but no command was supplied''.
* Ribosome binding site was correctly identified ''but no command was supplied''.
* Start codon was correctly identified ''but no command was supplied''.
* ''Stop codon was incorrectly identified because of a miscount in the base triplets.''
* ''The full hairpin structure of the terminator was missed, and no command was supplied.''
* ''The mRNA strand was incorrectly identified, and no command was supplied to indicate how you got this answer.''
* ''The amino acid sequence was incorrectly identified, and no command was supplied to indicate how you got this answer.''
In terms of your wiki link routine, your entries in the user and individual assignment pages were missing these items:
* Link from user page to shared journal page.
* Correct page name for individual assignment page. (i.e., the name of the page was incorrect)
* A link from your user page to the [[Week 4]] assignment.
* A link from your individual assignment page back to your user page.
* Category designation for your individual assignment page.
Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:28, 24 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* I did not see an entry in the [[Class_Journal_Week_5 | Week 5 shared class reflection.]]
* Your individual journal entry (UniProt Exercise) was submitted late.
* Your electronic lab notebook did not contain enough detail such that you or another person could reproduce what you did using only the information from your journal entry. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Look at some of your classmates' entries to see some examples and please let us know if you have any questions.
* Remember to link your use page to the assignment page, your journal page back to your user page, and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.
* The name for your journal entry page should be "Mmalefyt Week 5", not "Individual HW week 5". Please correct this moving forward in the class.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:08, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, there were equal contributions from each student to this page.
* You need to link from the database wiki page to the [[Class Journal Week 5]] page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:18, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* I’m going to chalk this up to a typo because you still reached the right answer; still, in the query for movies whose titles begin with the word “Star,” the space at the end of the ''"^Star"'' pattern is missing—this would match more rows than desired, because without the space, your query will also get movies whose titles start with the words “Stare,” “Startle,” “Stark,” or “Start,” to name a few. As mentioned, though, your count still emerges correctly, so I think you did type the correct query in but mistranscribed it into the wiki page.
* For the query requesting movie counts in the 1940s by year, the query supplied is a non-starter because the ''select-from'' portion is incorrect. You still got some answers, so this might be a mistranscription as well, in which case—double-check what you write into the wiki page! The posted answer remains incomplete, however, because it does not include the years associated with each count. Note how you list 9 numbers, but there are ''10'' years from 1940 to 1949! One year had zero movies—which one?
* The 6th query explicitly requests that the movie titles be alphabetized, but your answer does not include this.
* Your last query also does not work as-is because it is missing the ''from'' clause—and I suspect that this was ''not'' a mistranscription because no answer was provided. The query has an additional issue, in that you don't really need the ''inner join'' with the ''rating'' table and yet this is included in the SQL. In some cases, an unnecessary join may change the answers that you get back.
* All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, these items were missing or not to-spec:
* Missing link from user page to shared journal page
* Incorrect name for your individual journal page
* Missing link from user page to [[Week 6]] assignment page
* Missing link from the journal page back to your user page
* Missing “Journal Entry” category on your journal page
These requested links and features make the navigation of your wiki work as easy as possible, so please make a habit of this.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 11:59, 12 October 2013 (PDT)

User talk:Laurmagee

2013-11-29T21:27:51Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* You listed the four file versions specified by the testing report template.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 13:27, 29 November 2013 (PST)

== Week 1 Feedback ==

You’re off to a decent start; just need to check off a few more wiki skills like file/image uploads, categories, and templates.

'''Items for completion/follow-up:'''
* Snail mail address
* Create a new wiki page
* Link to an external site
* Create a numbered list
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Assign a category to a page
* Create and use a template
* Link to an assignment (Week ''n'') page
* Link to the shared journal from your user page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:06, 3 September 2013 (PDT)

=== Week 1 Feedback Follow-up ===

Hi Lauren,

Thanks for filling in the missing information/wiki skill items from last week! As for the two leftovers that weren’t clear, here’s my stab at explaining them further...

“Comments inside the wiki markup” refer to text that you can “hide” in your wiki page, which is only visible when the user is editing it. In other words, these can be “comments” by you that are not meant to be part of the content of the page. If you edit this Talk page, you will see that, right below this paragraph, there is text in the source that you do not see on the page.

Note the starting and ending symbols—that’s how you tell the wiki that whatever is in between should only be visible during editing.

Now, as for the Category, look at my [[User:Dondi|user page]] and scroll to the bottom. There is a box that starts with “Categories:” with red links for Individual Homework and User Page. This is what is meant by a category. It is a “tag” that you can attach to a page, so that it can be accessed by category. If you click on Individual Homework or User Page, you will see other pages that have been given that category. Your Shared Journal pages have this also.

Hope this answers your questions. Let me know if more explaining is needed.

One last point of feedback, and that is regarding your template—you certainly got the mechanics of it right (creating; using). Do try to build it up as a table of contents for your work and other related pages—this is a very compelling use for a template, particularly with the way we are using the wiki.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:59, 7 September 2013 (PDT)

== Week 2 Feedback ==

* The timestamp on your assignment showed that it was completed two minutes after midnight. Make sure in the future that you start the assignment early enough so that you can submit it on time.
* You need to post your answers to the individual part of the assignment on a different page than the class journal page. Name your new page ''username week #''. For example, this week's assignment should have been on a page called ''Laurmagee week 2''. Please create this page and copy the content over to it. You will also need to be mindful that you need to create a series of links:
*# Link your user page to your individual journal page.
*# Link your individual journal page back to your user page.
*# Add the category "Journal Entry" to your individual journal page.
*#* Note that you can add the three links above to your template. That way, you can use your template each time and not have to worry about forgetting to make the requested links.
* As discussed in class, you had two missing amino acids and you need to use "M", or "Met" for methionine, not "start".
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections requested above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* I saw from your class journal entry that you are still not clear on the elements of a gene (promoter/terminator), etc. Please talk to me about this in office hours because it will be necessary to know this to complete the computer lab exercises this week and next.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:38, 11 September 2013 (PDT)''

P.S. I answered your question on my user talk page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:12, 12 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making the corrections to your translation, moving your page, and adding the requested links. However, the category is still missing from this page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:03, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Your experience with “Where’s my stuff” typically occurs when a computing system is strongly protecting file extensions like ''.txt'' and ''.html''. Different operating systems apply protections differently. Typically, there is a setting one can hit that tells the computer that you know what you are doing with respect to these extensions, after which you will then have greater control over these. In any case, nothing to worry about; what matters is that you got a sense for what role these file extensions play.
* Your '''sed''' and '''match''' skills are great! All of your commands were correct, save for what I will chalk up to a typo in your '''sed''' commands: the portion that is meant to separate the nucleotides into triplets is missing a space after the '''&''' character. This space is very important, because it enforces the triplet grouping of the bases. At the same time, spaces are also easy to miss, so keep a close eye on what lands on your wiki from your command window.
* Your journal answer page was missing the requested ''Journal Entry'' category—please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:18, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* ''-35 box was almost correctly identified but there was a space missing in one of your commands.''
* ''-10 box command did not refine the search pattern to highlight the correct one (there were two possibilities and the only way to distinguish one from the other was to identify the one that came after the -35 box).''
* ''Your transcription start site command counted off the -10 box in the wrong direction.''
* Ribosome binding site was correctly identified with an appropriate command, ''but the first to statements of that command had a typo (missing '''g''')''.
* Start codon was correctly identified with an appropriate command.
* ''Stop codon was not correctly identified by the provided command (it missed counting off in threes from the start codon).''
* ''You missed the full hairpin sequence of the terminator.''
* ''The incorrect mRNA strand was identified, and no command was provided to indicate where things might have gone wrong.''
* ''The incorrect amino acid sequence was identified, and no command was provided to indicate where things might have gone wrong.''
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:19, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* The missing ''Journal Entry'' category in your Week 3 journal answer page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:02, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was an adequate description of what you did, although you listed the identifier for the EGFR protein incorrectly. Also, I think you were mixing up the PDB and PubMed databases.
* Moving forward starting with the [[Week 8]] assignment, this will be an important part of each weekly assignment. Keep in mind the guideline that you or someone else should be able to reproduce what you did using only the information on your journal entry page. Your page could have been enhanced by providing hyperlinks to the pages you visited and by showing one or more screenshots from your database exploration.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:12, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* This assignment is incomplete; I did not find a wiki page for GeneDB, am I missing something? ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:02, 11 October 2013 (PDT)''

== Week 6 Feedback ==

Thank you for submitting everything super early!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* In your movies-beginning-with-the-word-“Star” query, you miss adding a space at the end of the ''"^Star"'' pattern—this matches more rows than desired, because without the space, your query will also get movies whose titles start with the words “Stare,” “Startle,” “Stark,” or “Start,” to name a few.
* The 5th and 8th queries, which request counts by certain categories (year in the 5th query; rating in the 8th), require a ''group by'' clause in order to deliver the answers with maximum efficiency. Your answer to the 5th query involves multiple separate retrievals, where the use of ''group by'' would reduce that to a single one; your answer to the 8th query returns the “lump sum” count, and not the count for each individual rating.
* The 7th query does not include the name of the ''member''s who submitted each rating; this information was explicitly requested.
* All your other database queries were correct and properly documented.
Your standardized wiki links and elements are all there except for the link from the journal page to the user page. Try to maintain a “flight check” list of these items (note how they are listed in every assignment) so that this becomes as worry-free as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 11:46, 12 October 2013 (PDT)

User talk:Gleis

2013-11-29T21:25:54Z

Dondi: Add signature line.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access, but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for the link from your journal entry page back to your user page.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 13:25, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I reviewed your Excel spreadsheet. Your <code>.xls</code> file only had the "forGenMAPP" in it; the other sheets where you did your calculations were not there. I noticed an error in the results of your TSTAT and p value calculations, but because the other sheets weren't there, I wasn't able to discern what went wrong. I hope that you have the <code>.xls</code> file somewhere so that you can go back to it and fix the errors. If not, you will need to either redo the calculations or get the file from your partner. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:51, 14 October 2013 (PDT)''
* Also, your syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of <nowiki>[[File:filename]] use [[Media:filename]]</nowiki>. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:59, 14 October 2013 (PDT)''
* Finally, please follow the convention for naming your files given in the assignment, so that it is maximally informative as to the contents. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:39, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Great coverage of the checklist! If you haven’t done independent research, still say so explicitly, just so we know you haven’t forgotten. Experimentation with "raw" HTML is noted—your mixing and matching of raw HTML with wiki markup is noted.

'''Items for completion/follow-up:'''
* Independent research
* Change summaries—try to enter these more consistently.
* Link to an assignment (Week ''n'') page
* Link to the shared journal from your user page (you have almost a link there, but not a fully accurate one)

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:00, 3 September 2013 (PDT)

I have answered your question on my user [[User talk:Kdahlquist | talk]] page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:03, 5 September 2013 (PDT)''

=== Week 1 Follow-Up Feedback ===

Thank you for catching up on the missing information/wiki skills from last week! You haven’t yet gotten totally consistent with entering a change summary whenever you edit a wiki page, so try to keep that in mind as you log more hours with the wiki.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:18, 7 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* Your translations were correct, but you needed to continue translating beyond the stop codons.
* The +3 frame was not an open reading frame.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* The Nirenberg article was written for other practicing biochemists and was also written as a memoir, so it is understandable that it was difficult to read.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:07, 11 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:58, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Your experience with “Where’s my stuff” typically occurs when a computing system is strongly protecting file extensions like ''.txt'' and ''.html''. Different operating systems apply protections differently. Typically, there is a setting one can hit that tells the computer that you know what you are doing with respect to these extensions, after which you will then have greater control over these. In any case, nothing to worry about; what matters is that you got a sense for what role these file extensions play.
* Your '''sed''' and '''match''' skills are great! All of your commands were correct.
* You were missing a number of requested links and wiki elements:
** Your user page was missing a link to the [[Week 3]] assignment page
** Your journal answer page was missing a link back to your user page
** Your journal answer page was also missing the requested ''Journal Entry'' category
:Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:55, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* Transcription start site was correctly identified ''but the command you used does not reflect the consensus information—you based your '''sed''' directive on the ribosome binding site and not the -10 box''.
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* ''Stop codon does not correctly count off in triplets after the start codon.''
* ''Terminator did not correctly include the full hairpin.''
* You correctly stated the mRNA strand, ''although you had to do some manual editing from your command''.
* ''The amino acid sequence was not correctly identified due to the issue with locating the stop codon.''
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:01, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* The missing link from your user page to the [[Week 3]] assignment page has been added.
* The missing link from your Week 3 journal answer page to your user page has been added.
* The missing ''Journal Entry'' category in your Week 3 journal answer page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:54, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook did not contain enough detail such that you or another person could reproduce what you did using only the information from your journal entry. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Look at some of your classmates' entries to see some examples and please let us know if you have any questions.
* Remember to link your journal page back to your user page and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:17, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your database wiki page was complete and thorough, although it looks like some final tweaks were completed after the deadline. It appears that both of you contributed equally to the page.
* You are missing a link from your user page to this database wiki page. Please add it to your template.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:12, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* In your movies-beginning-with-the-word-“Star” query, you miss adding a space at the end of the ''"^Star"'' pattern—this matches more rows than desired, because without the space, your query will also get movies whose titles start with the words “Stare,” “Startle,” “Stark,” or “Start,” to name a few.
* Your last, individual query has a ''group by title'' clause, but that clause is not actually necessary because you aren’t performing computations like ''count'' or ''average''. In some cases, a superfluous ''group by'' may produce incorrect results; it just so happens that in your particular query, it does not have a detrimental effect.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:59, 11 October 2013 (PDT)

User talk:Vkuehn

2013-11-29T21:25:28Z

Dondi: Add signature line.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access, but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 13:25, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I have reviewed the files you uploaded. The contents are correct and ready to go for Tuesday.
* However, your syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of <nowiki>[[File:filename]] use [[Media:filename]].</nowiki>
* Also, please follow the convention for naming your files given in the assignment, so that it is maximally informative as to the contents. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". You need to add a date to your filename.

— ''[[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:47, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Great coverage! You missed just a few items. Make sure to do them to cover all the bases.

'''Items for completion/follow-up:'''
* Create a new wiki page
* Link to an external site
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Link to an assignment (Week ''n'') page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:54, 3 September 2013 (PDT)

=== Week 1 Follow-up Feedback ===

Thank you for filling in the missing wiki skills from last week! You missed that last one, “link to an assignment (Week ''n'') page.” You will find that having this link will become very convenient, particularly if you want to go back and forth between the assignment page itself and your answers.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:14, 7 September 2013 (PDT)

== Week 2 Journal Feedback ==

* Your journal assignment was partially late this week. You will be understandably busy this next week, but hopefully you will be able to get back on track submitting your assignments on time soon.
* Your translation had point mutations in frames +1 and +3; you had a deletion in frame -2; you did not continue your translation beyond the stop codons. The +3 frame did not have an open reading frame. You have the opportunity to earn back the points you missed this week by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections listed below. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* You are also missing some links on your pages. Specifically:
*# You need to link from your user page to the [[Week 2 | Week 2 Assignment]] page.
*# You need to link from your individual journal entry back to your user page.
*# You need to include the category "Journal Entry" on your individual journal page.
*#* You can easily make the corrections above by adding them to your template and then using your template on your user and individual journal entry pages, for this week and all future weeks.
* Yes, the Nirenberg article was quite dense, but I'm glad you enjoyed it anyway!
* I answered your question on my user talk page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:15, 10 September 2013 (PDT)''

=== Week 2 Follow-up ===

* I have reviewed the changes you made to your Week 2 journal entry. I note that you added the requested links via your template, but did not make any content corrections to your translation.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:02, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment by the deadline that you set for yourself!
* Good to hear that you succeeded in exerting control of your file extensions.
* Your '''sed''' skills need some practice and review—understandably so because of missed classes. Let’s see if we can catch you up with some face-to-face time when you are back:
** The complement command only works for a very specific nucleotide sequence, and not over all bases in general.
** Your +1 reading frame came out right, but +2 and +3 incorrectly performed the initial “chopping” of the first and first two bases, respectively. You weren’t deleting the bases outright, but replacing them with spaces. Unfortunately, the '''.''' placeholder also matches with spaces, and so you end up with incorrect triplets.
** For the -1, -2, and -3 reading frames, the command sequences you provided also contain the error in the above bullet, plus are missing the complement step.
* Your '''match''' and '''grep'''/'''wc''' results are completely on the money!
* You were missing a number of requested links and wiki elements:
** Your user page was missing a link to the shared journal page
** Your user page was also missing a link to the [[Week 3]] assignment page
:Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:29, 16 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to an assignment or wiki link checklist:
* Corrections to your +2, +3, -1, -2, and -3 reading frames. The -3 reading frame command has a typo, however: the “chopoff” '''sed''' command is missing a '''^''' in its match pattern.
* The link from your user page to the Week 3 shared journal page has been added.
* The link from your user page to the [[Week 3]] assignment page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:50, 29 September 2013 (PDT)

== Week 4 Feedback ==

Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon was correctly identified with an appropriate command.
* The terminator sequence was correctly identified.
* ''No mRNA strand was identified, and no command was provided to indicate what might have been tried.''
* ''No amino acid sequence was identified, and no command was provided to indicate what might have been tried.''
In terms of your wiki link routine, your entries in the user and individual assignment pages were missing these items:
* A link from your individual assignment page back to your user page.
* Category designation for your individual assignment page.
Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:35, 9 October 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was good, but still could be improved. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.
* Remember to link your journal page back to your user page and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:20, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, it looks like Kevin was the main contributor to this page.
* You need to link from the database wiki page to the [[Class Journal Week 5]] page.
* The main classification for Ensembl is that it is a sequence/ genome database.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:16, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The incorrect years were used in the query for movies released in the 1980s with 4 digits in their titles.
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* In your movies-beginning-with-the-word-“Star” query, note that the question was ''how many'' movies matched that. Thus, a ''count'' computation is required there.
* All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, a couple of items were missing:
* Link from the journal page back to your user page
* “Journal Entry” category on your journal page
These requested links and features make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 10:19, 12 October 2013 (PDT)

User talk:Lena

2013-11-29T21:25:08Z

Dondi: Add signature line.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* The file versions, as specified by the testing report template, are not all directly listed. You do state the dates for the files used, but some of them have specific versions also, as indicated by the host website. Ideally, that is the information to record.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* There is no indication that you successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access and compared its data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* An appropriate record was seen for the tasks performed, but for the one that was missed (PostgreSQL), an entry/note should have also been made about why this portion was not finished (e.g., technical difficulties, issues with the query, etc.).

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for inclusion of the ''Journal Entry'' category.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 13:25, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* I reviewed your .xls and .txt files from part 1 of the week 8 assignment. I know that we worked on your spreadsheet after class, but I still found some errors.
* On your sheet, "Scaled_Centered" there are errors in the standard deviation functions in cells C3 through M3. Your function has a range to row 5225, when it should be 5224. If you copy and paste the formula from cell B3 to the rest, that should fix that problem.
* On your sheet, "Statistics", there are errors in the Avg_LogFC_A, Avg_LogFC_B, and Avg_LogFC_C columns. The ranges over which you calculate the averages are incorrect. For example Avg_LogFC_A should be
=AVERAGE(B2:E2)
* Your TSTAT calculation also specifies the incorrect range. The correct range is N2:P2 for the first cell.
* Please make these corrections and re-upload your files. Alternately, you can work with your partner to get the correct file.
* Also, please follow the convention for naming your files given in the assignment. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". At minimum, your filename needs to have a date included.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:21, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Great coverage! You missed just a few items. And don’t forget to send us your email with questions/concerns.

'''Items for completion/follow-up:'''
* Email worries/questions/concerns or anything else you’d like us to know
* Create a new wiki page
* Comments inside the wiki markup
* Use a template
* Link to an assignment (Week ''n'') page
* Place your signature in the shared journal page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:50, 3 September 2013 (PDT)

=== Week 1 Follow-Up Feedback ===

Thank you for filling in the blanks from last week! Your confusion about templates is noted (as you stated in your commented-out markup)—however, you are indeed using your template correctly in the user page. Think of a template as a “live shortcut.” It lets you repeat the same piece of wiki all over the place, and whenever you edit that piece of wiki, it automatically updates everywhere. Let us know if further confusion remains.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:10, 7 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* Your translations were all correct; frame +3 does not contain an open reading frame, though.
* You will need to work on completing/correcting the links requested as part of the assignment. Specifically:
*# We have a specific naming convention that we would like you to use when naming your new individual journal pages. You should name them ''username week #''; for example your week 2 assignment page should be named ''Lena Week 2'', instead of "Genetic Code Assignment". You will need to '''''move''''' the contents of your "Genetic Code Assignment" page to your "Lena Week 2" page, for which you have a redlink on your user page. To do so, follow the directions listed [http://en.wikipedia.org/wiki/How_to_move_a_page here]]. We will be happy to talk you through this in class or office hours if you like. For the future, please make sure you are using the preferred naming convention for new pages.
*# You are missing the link from your User page to the [[Week 2 | Week 2 Assignment]] page.
*# You are missing the link from your individual week 2 journal entry back to your User page.
*# You need to add the category "Journal Entry" to your individual week 2 journal entry page. We are not actually using the category "Individual Homework" like Dr. Dionisio demo'd in class; we apologize for any confustion this caused.
*#* For the three items above, you can add these links to your template and then just use your template on your user page and all journal entry pages. That way, you won't forget to put the links in future assignments.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections requested above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* Yes, the Nirenberg article was quite dense and written as a memoir as opposed to expository text.
* I have also answered your question on my user talk page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:59, 10 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:57, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Good to hear that you succeeded in exerting control of your file extensions.
* You missed the '''cat''' command at the beginning of your reading frame answers. This is not a huge deal, but remember how attention to detail is a very important part of working with computers.
* Your '''sed''' and '''match''' skills are otherwise great! All of your commands were correct.
* Regarding the '''match''' question comparing it to '''grep'''/'''wc''', you missed reporting on how many of the matched pattern were found. For the third question, the distinction we were looking for is the way '''grep'''/'''wc''' can only count lines, thus missing cases where a pattern appears more than once in a single line.
* Your journal page was missing the requested ''Journal Entry'' category. Again falling under the “attention to detail” heading, please note the bulleted checklist provided under the assignment headings.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:50, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* ''-35 box was missed due to an extra slash in your '''sed''' command.''
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was incorrectly identified.''
* Ribosome binding site was correctly identified with an appropriate command.
* Your start codon was correctly identified with an appropriate command in the integrated all-in-one version, ''but is missing the added new line in the separate answer bullet.''
* ''Your stop codon command was never finalized.''
* The terminator was correctly identified with an appropriate command.
* ''Your mRNA strand is incorrect, and no command was supplied to show how you got your answer.''
* You determined the correct amino acid sequence ''but no command was supplied to show how you got your answer''.
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:49, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* Missing Journal Entry category from Week 3 journal page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:43, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was a thorough description of what you did. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:22, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, there were equal contributions from each student to this page.
* You need to link from the database wiki page to the [[Class Journal Week 5]] page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:19, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query had the '''nowiki''' tags in the incorrect position—they should be completely surrounding the four apostrophes (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* Your last, individual query joins the ''member'' table, but that table is not actually necessary. When working with databases, we are sensitive to doing more work than necessary, because sometimes this additional work strongly detracts from speed, particularly if the tables contain large numbers of rows. An extra but unnecessary join will also, in some cases, change the results that you get back.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 11 October 2013 (PDT)

User talk:HDelgadi

2013-11-29T21:24:48Z

Dondi: Add signature line.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access and compared its data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 13:24, 29 November 2013 (PST)

== Week 8 Feedback ==

* I have reviewed your .xls and .txt files from part 1 of the Week 8 assignment. They are correct and ready to go for Tuesday. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:27, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You did generally well for this first time out; do complete the wiki checklist and be consistent with summaries, as much as possible.

'''Items for completion/follow-up:'''
* Snail mail address
* Change summaries—try to enter these more consistently.
* Create a new wiki page
* Link to an external site
* Create a numbered list
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Create and use a template
* Link to an assignment (Week ''n'') page
* Link to the shared journal from your user page
* Place your signature in the shared journal page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:44, 3 September 2013 (PDT)

=== Week 1 Follow-Up ===

Thanks very much for completing your wiki checklist! Some notes on your latest work:
* You did the HHMI external link technically correctly, but notice how it appears as [http://cse.lmu.edu/programs/hhmi/] on your page. You can give this link some custom text by adding a space after the address, and putting the text after that space, [http://cse.lmu.edu/programs/hhmi/ like this] (edit this page to see how it was done).
* Your confusion about templates is noted (I saw that in your commented-out wiki markup!). You are creating it right; your confusion has to do with using it. Well, I’m using it down here:

(your template starts below)

{{HDelgadi}}

(your template just ended above)

:...note the curly braces (when you edit this page) and the removal of “Template:” That’s it! Whenever you write this into a wiki page, your template will show up there instead.

* Finally, you still have not “signed” your shared journal entries, but I know you can do the signature because you did it when you left a question on [[Talk:Dondi|my]] and [[Talk:Kdahlquist|Dr. Dahlquist’s]] talk pages. Make sure you do that on your shared journal entries too; it gives your reflection responses more of that “journal entry” feel.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:28, 7 September 2013 (PDT)

== Week 2 Journal Feedback ==

* Thank you for submitting your assignment on time.
* As noted in class, you had a couple of "point mutations" in frames +2 and +3.
* Remember to add the category "journal entry" to your individual journal page. If you add this category to your template and then use the template on your page, you will always remember to fulfill this part of your assignment.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the correction listed above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* To answer your question about the Nirenberg reading, he was talking about the solubility of polyphenylalanine because he wanted to make sure that the product that was translated from the poly(U) was the same thing as a lab standard of polyphenylalanine. So he had to learn about that to make sure that they were the identical chemical.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:52, 10 September 2013 (PDT)''

P.S. I answered your question on my [[User talk:Kdahlquist|talk]] page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:55, 10 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making the corrections to your translation.
* The category is still missing for this page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:56, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Your experience with “Where’s my stuff” typically occurs when a computing system is strongly protecting file extensions like ''.txt'' and ''.html''. Different operating systems apply protections differently. Typically, there is a setting one can hit that tells the computer that you know what you are doing with respect to these extensions, after which you will then have greater control over these. In any case, nothing to worry about; what matters is that you got a sense for what role these file extensions play.
* Your '''sed''' and '''match''' skills are great! All of your commands were correct.
* Regarding the '''match''' question on "James," note that these look very much like names, so it is safe to guess that this search pattern may indicate a scientist or author (given the type of file you were searching).
* Your user page was missing a link to the [[Week 3]] assignment page. Strongly consider using a template for this, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:40, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon was correctly identified with an appropriate command.
* ''You missed that the terminator includes 4 additional base pairs after the hairpin.''
* ''Your mRNA strand is short—you only returned the start-to-stop codon, but transcription actually goes from the transcription start site to the end of the terminator.''
* You determined the correct amino acid sequence with an appropriate command.
In terms of your wiki link routine, everything was there except for:
* A link from your user page to the [[Week 4]] assignment.
Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:36, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* A link from your user page to the Week 4 assignment was added

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:40, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was a good description of what you did, but the formatting could be improved to be cleaner and easier to read. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:23, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, it appears that Mitchell was the main contributor to this page.
* I see that you used a template to move this page content to one with the proper name. There is a better way to move pages, see the drop down arrow next to the "View history" tab at the top of the page.
* Be careful about the formatting of your hyperlinks. Only use two square brackets when linking to internal wiki pages; external links use only single square brackets. Also, the numbering of your page with respect to the questions is off.
* You could have elaborated a bit more on your answers to the questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:22, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting within your self-imposed extended deadline!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* For the query requesting data on all movies, ratings, and members, you return more columns/fields than specifically requested. When working with databases, we are sensitive to doing more work than necessary, because sometimes this additional work strongly detracts from speed, particularly if the tables contain large numbers of rows.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:03, 11 October 2013 (PDT)

User talk:Slouie

2013-11-29T21:24:15Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You noted that there were problems with your .gdb file to the wiki, but by all accounts this was most likely a transient problem, and there is no indication that you went back and tried to upload the file again.
* You successfully ran the Tally Engine.
* You appear to have successfully run xmlpipedb-match, but reported only the results without posting primary documentation of this activity (e.g., screenshots, exact numeric output).
* There is no indication that you successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access, but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for the link from your journal entry page back to your user page and inclusion of the ''Journal Entry'' category.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 13:24, 29 November 2013 (PST)

== Week 8 Interim Feedback ==

* Your files are correct and ready to go for Tuesday. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:49, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You did generally well for this first time out; do complete the wiki checklist and be consistent with summaries, as much as possible. You were also very close with the template—everything is properly linked but you just have to create the template content itself.

'''Items for completion/follow-up:'''
* Snail mail address
* Upper division coursework—say “none” if you haven’t taken any.
* Create a new wiki page
* Link to an external site
* Create a numbered list
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Create a template
* Link to an assignment (Week ''n'') page
* Link to the shared journal from your user page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:03, 3 September 2013 (PDT)

=== Week 1 Follow-up Feedback ===

Thank you very much for completing all missing information/wiki skills! Here’s to building on these skills as the course progresses.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 7 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* As we discussed in class, your translation of all six frames was incorrect. There was probably a mistake in the sequence or it was translated in the wrong direction. Please use the ExPaSY tool to translate it and figure out where you went wrong. As was noted in class, you have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* The Nirenberg article was written for other practicing biochemists and from a memoir point of view, so it is understandible that you found it difficult.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:12, 11 September 2013 (PDT)''

P.S. I answered your queston on my user talk page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:12, 12 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:58, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Good to hear that you succeeded in exerting control of your file extensions.
* Your '''sed''' and '''match''' skills are great with the exception of your 3'-5' reading frame commands—you missed doing a complement on those bases.
* For the third '''match''' question, you missed that the command was supposed to have run on the ''hs_ref_GRCh37_chr19.fa'' file, not ''493.P_falciparum.xml''. The commands were still successful and you made the correct inference about how '''match''' and '''grep'''/'''wc''' are different, but you were using different data from what was specified.
* You were missing a number of requested links and wiki elements:
** Your journal answer page was missing a link back to your user page
** Your journal answer page was also missing the requested ''Journal Entry'' category
:Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed. Additional props, though, for having your shared journal link go directly to your entry as opposed to the overall page.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:10, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon was correctly identified with an appropriate command.
* The terminator sequence was correctly identified ''but the command used to identify it makes more assumptions than were given in the consensus information''.
* Your mRNA strand included the correct range of bases but ''was complemented when it should not have been''.
* You determined the correct amino acid sequence with an appropriate command.
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:06, 24 September 2013 (PDT)

== Group work ==

Hey Stephen,
Unfortunately I won't be able to make it to the library today.
I did however set up the database and most of the questions needed
for it. If you could finish those up for us I think we should be good
at least for the journal tonight. We can set up another meeting to finish the other work.
Feel free to contact me.
3109412298

== Makeup Point Update ==

You have been credited for making the following change(s) to an assignment or wiki link checklist:
* Your 3'-5' reading frame commands now correctly apply a complement to their bases.
* For the third '''match''' question, you have updated your reported results so that they are now based on the ''hs_ref_GRCh37_chr19.fa'' file, not ''493.P_falciparum.xml''.
* The missing link from your Week 3 journal answer page back to your user page has been added.
* The missing ''Journal Entry'' category in your Week 3 journal answer page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:00, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was an adequate description of what you did. Moving forward starting with the [[Week 8]] assignment, this will be an important part of each weekly assignment. Keep in mind the guideline that you or someone else should be able to reproduce what you did using only the information on your journal entry page. Your page could have been enhanced by providing hyperlinks to the pages you visited and by showing one or more screenshots from your database exploration. See some of your classmates' pages for how they did this.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:15, 8 October 2013 (PDT)''

=== Database Wiki Feedback ===

* Thank you for submitting your assignment on time. From the history, it looks like Alina was the main contributor to this page. This appears to be borne out by the fact that there are links missing from your user page to this page and from the database wiki page to your user page.
* You could have been more specific as to which species were covered in the database.
* OrganelleDB is not an example of a community database, a community database is basically like this wiki where a distributed set of users enters information directly into the database. Instead, OrganelleDB is an example of a specialty database.
* You could have provided more information about the sample query you tried.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:09, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* I’m going to chalk this up to a typo because you still reached the right answer; still, in the query for movies whose titles begin with the word “Star,” you have a '''%''' wildcard that should not be there. '''%''' is for use with ''like'' but not with '''~'''.
* The 5th query, which requests counts by year, is much easier to answer if you include ''year'' in the ''select'' clause. What you have still produces the right answer, but you have to be careful in determining which count pertains to which year. In particular, what if there was a year with zero movies? That might be missed in the tallies.
* The 8th query, which requests for counts by rating, highlights this issue even more. Here, the query is missing the ''group by'' clause. Thus, you needed to manually tally up the number of movies that got each individual rating. This was manageable for the small data set, but becomes unwieldy with large ones.
* The 9th query, which seeks the average rating for movies beginning with the word “Star,” has the same typo from the 4th query. This time, however, the incorrect average is reached.
* All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, all is well except for a small oversight: your “Journal Entry” category was encoded as a wiki page, and not a Category.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 11:37, 12 October 2013 (PDT)

User talk:Gleis

2013-11-29T21:13:14Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access, but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for the link from your journal entry page back to your user page.

== Week 8 Interim Feedback ==

* I reviewed your Excel spreadsheet. Your <code>.xls</code> file only had the "forGenMAPP" in it; the other sheets where you did your calculations were not there. I noticed an error in the results of your TSTAT and p value calculations, but because the other sheets weren't there, I wasn't able to discern what went wrong. I hope that you have the <code>.xls</code> file somewhere so that you can go back to it and fix the errors. If not, you will need to either redo the calculations or get the file from your partner. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:51, 14 October 2013 (PDT)''
* Also, your syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of <nowiki>[[File:filename]] use [[Media:filename]]</nowiki>. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:59, 14 October 2013 (PDT)''
* Finally, please follow the convention for naming your files given in the assignment, so that it is maximally informative as to the contents. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:39, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Great coverage of the checklist! If you haven’t done independent research, still say so explicitly, just so we know you haven’t forgotten. Experimentation with "raw" HTML is noted—your mixing and matching of raw HTML with wiki markup is noted.

'''Items for completion/follow-up:'''
* Independent research
* Change summaries—try to enter these more consistently.
* Link to an assignment (Week ''n'') page
* Link to the shared journal from your user page (you have almost a link there, but not a fully accurate one)

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:00, 3 September 2013 (PDT)

I have answered your question on my user [[User talk:Kdahlquist | talk]] page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:03, 5 September 2013 (PDT)''

=== Week 1 Follow-Up Feedback ===

Thank you for catching up on the missing information/wiki skills from last week! You haven’t yet gotten totally consistent with entering a change summary whenever you edit a wiki page, so try to keep that in mind as you log more hours with the wiki.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:18, 7 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* Your translations were correct, but you needed to continue translating beyond the stop codons.
* The +3 frame was not an open reading frame.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* The Nirenberg article was written for other practicing biochemists and was also written as a memoir, so it is understandable that it was difficult to read.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:07, 11 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:58, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Your experience with “Where’s my stuff” typically occurs when a computing system is strongly protecting file extensions like ''.txt'' and ''.html''. Different operating systems apply protections differently. Typically, there is a setting one can hit that tells the computer that you know what you are doing with respect to these extensions, after which you will then have greater control over these. In any case, nothing to worry about; what matters is that you got a sense for what role these file extensions play.
* Your '''sed''' and '''match''' skills are great! All of your commands were correct.
* You were missing a number of requested links and wiki elements:
** Your user page was missing a link to the [[Week 3]] assignment page
** Your journal answer page was missing a link back to your user page
** Your journal answer page was also missing the requested ''Journal Entry'' category
:Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:55, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* Transcription start site was correctly identified ''but the command you used does not reflect the consensus information—you based your '''sed''' directive on the ribosome binding site and not the -10 box''.
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* ''Stop codon does not correctly count off in triplets after the start codon.''
* ''Terminator did not correctly include the full hairpin.''
* You correctly stated the mRNA strand, ''although you had to do some manual editing from your command''.
* ''The amino acid sequence was not correctly identified due to the issue with locating the stop codon.''
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:01, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* The missing link from your user page to the [[Week 3]] assignment page has been added.
* The missing link from your Week 3 journal answer page to your user page has been added.
* The missing ''Journal Entry'' category in your Week 3 journal answer page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:54, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook did not contain enough detail such that you or another person could reproduce what you did using only the information from your journal entry. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Look at some of your classmates' entries to see some examples and please let us know if you have any questions.
* Remember to link your journal page back to your user page and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:17, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your database wiki page was complete and thorough, although it looks like some final tweaks were completed after the deadline. It appears that both of you contributed equally to the page.
* You are missing a link from your user page to this database wiki page. Please add it to your template.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:12, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* In your movies-beginning-with-the-word-“Star” query, you miss adding a space at the end of the ''"^Star"'' pattern—this matches more rows than desired, because without the space, your query will also get movies whose titles start with the words “Stare,” “Startle,” “Stark,” or “Start,” to name a few.
* Your last, individual query has a ''group by title'' clause, but that clause is not actually necessary because you aren’t performing computations like ''count'' or ''average''. In some cases, a superfluous ''group by'' may produce incorrect results; it just so happens that in your particular query, it does not have a detrimental effect.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:59, 11 October 2013 (PDT)

User talk:Vkuehn

2013-11-29T21:09:44Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access, but did not compare the data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

== Week 8 Interim Feedback ==

* I have reviewed the files you uploaded. The contents are correct and ready to go for Tuesday.
* However, your syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of <nowiki>[[File:filename]] use [[Media:filename]].</nowiki>
* Also, please follow the convention for naming your files given in the assignment, so that it is maximally informative as to the contents. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". You need to add a date to your filename.

— ''[[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:47, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Great coverage! You missed just a few items. Make sure to do them to cover all the bases.

'''Items for completion/follow-up:'''
* Create a new wiki page
* Link to an external site
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Link to an assignment (Week ''n'') page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:54, 3 September 2013 (PDT)

=== Week 1 Follow-up Feedback ===

Thank you for filling in the missing wiki skills from last week! You missed that last one, “link to an assignment (Week ''n'') page.” You will find that having this link will become very convenient, particularly if you want to go back and forth between the assignment page itself and your answers.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:14, 7 September 2013 (PDT)

== Week 2 Journal Feedback ==

* Your journal assignment was partially late this week. You will be understandably busy this next week, but hopefully you will be able to get back on track submitting your assignments on time soon.
* Your translation had point mutations in frames +1 and +3; you had a deletion in frame -2; you did not continue your translation beyond the stop codons. The +3 frame did not have an open reading frame. You have the opportunity to earn back the points you missed this week by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections listed below. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* You are also missing some links on your pages. Specifically:
*# You need to link from your user page to the [[Week 2 | Week 2 Assignment]] page.
*# You need to link from your individual journal entry back to your user page.
*# You need to include the category "Journal Entry" on your individual journal page.
*#* You can easily make the corrections above by adding them to your template and then using your template on your user and individual journal entry pages, for this week and all future weeks.
* Yes, the Nirenberg article was quite dense, but I'm glad you enjoyed it anyway!
* I answered your question on my user talk page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:15, 10 September 2013 (PDT)''

=== Week 2 Follow-up ===

* I have reviewed the changes you made to your Week 2 journal entry. I note that you added the requested links via your template, but did not make any content corrections to your translation.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:02, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment by the deadline that you set for yourself!
* Good to hear that you succeeded in exerting control of your file extensions.
* Your '''sed''' skills need some practice and review—understandably so because of missed classes. Let’s see if we can catch you up with some face-to-face time when you are back:
** The complement command only works for a very specific nucleotide sequence, and not over all bases in general.
** Your +1 reading frame came out right, but +2 and +3 incorrectly performed the initial “chopping” of the first and first two bases, respectively. You weren’t deleting the bases outright, but replacing them with spaces. Unfortunately, the '''.''' placeholder also matches with spaces, and so you end up with incorrect triplets.
** For the -1, -2, and -3 reading frames, the command sequences you provided also contain the error in the above bullet, plus are missing the complement step.
* Your '''match''' and '''grep'''/'''wc''' results are completely on the money!
* You were missing a number of requested links and wiki elements:
** Your user page was missing a link to the shared journal page
** Your user page was also missing a link to the [[Week 3]] assignment page
:Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:29, 16 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to an assignment or wiki link checklist:
* Corrections to your +2, +3, -1, -2, and -3 reading frames. The -3 reading frame command has a typo, however: the “chopoff” '''sed''' command is missing a '''^''' in its match pattern.
* The link from your user page to the Week 3 shared journal page has been added.
* The link from your user page to the [[Week 3]] assignment page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:50, 29 September 2013 (PDT)

== Week 4 Feedback ==

Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon was correctly identified with an appropriate command.
* The terminator sequence was correctly identified.
* ''No mRNA strand was identified, and no command was provided to indicate what might have been tried.''
* ''No amino acid sequence was identified, and no command was provided to indicate what might have been tried.''
In terms of your wiki link routine, your entries in the user and individual assignment pages were missing these items:
* A link from your individual assignment page back to your user page.
* Category designation for your individual assignment page.
Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:35, 9 October 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was good, but still could be improved. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.
* Remember to link your journal page back to your user page and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:20, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, it looks like Kevin was the main contributor to this page.
* You need to link from the database wiki page to the [[Class Journal Week 5]] page.
* The main classification for Ensembl is that it is a sequence/ genome database.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:16, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The incorrect years were used in the query for movies released in the 1980s with 4 digits in their titles.
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* In your movies-beginning-with-the-word-“Star” query, note that the question was ''how many'' movies matched that. Thus, a ''count'' computation is required there.
* All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, a couple of items were missing:
* Link from the journal page back to your user page
* “Journal Entry” category on your journal page
These requested links and features make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 10:19, 12 October 2013 (PDT)

User talk:Lena

2013-11-29T21:07:50Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* The file versions, as specified by the testing report template, are not all directly listed. You do state the dates for the files used, but some of them have specific versions also, as indicated by the host website. Ideally, that is the information to record.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* There is no indication that you successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access and compared its data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* An appropriate record was seen for the tasks performed, but for the one that was missed (PostgreSQL), an entry/note should have also been made about why this portion was not finished (e.g., technical difficulties, issues with the query, etc.).

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for inclusion of the ''Journal Entry'' category.

== Week 8 Interim Feedback ==

* I reviewed your .xls and .txt files from part 1 of the week 8 assignment. I know that we worked on your spreadsheet after class, but I still found some errors.
* On your sheet, "Scaled_Centered" there are errors in the standard deviation functions in cells C3 through M3. Your function has a range to row 5225, when it should be 5224. If you copy and paste the formula from cell B3 to the rest, that should fix that problem.
* On your sheet, "Statistics", there are errors in the Avg_LogFC_A, Avg_LogFC_B, and Avg_LogFC_C columns. The ranges over which you calculate the averages are incorrect. For example Avg_LogFC_A should be
=AVERAGE(B2:E2)
* Your TSTAT calculation also specifies the incorrect range. The correct range is N2:P2 for the first cell.
* Please make these corrections and re-upload your files. Alternately, you can work with your partner to get the correct file.
* Also, please follow the convention for naming your files given in the assignment. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". At minimum, your filename needs to have a date included.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:21, 14 October 2013 (PDT)''

== Week 1 Feedback ==

Great coverage! You missed just a few items. And don’t forget to send us your email with questions/concerns.

'''Items for completion/follow-up:'''
* Email worries/questions/concerns or anything else you’d like us to know
* Create a new wiki page
* Comments inside the wiki markup
* Use a template
* Link to an assignment (Week ''n'') page
* Place your signature in the shared journal page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:50, 3 September 2013 (PDT)

=== Week 1 Follow-Up Feedback ===

Thank you for filling in the blanks from last week! Your confusion about templates is noted (as you stated in your commented-out markup)—however, you are indeed using your template correctly in the user page. Think of a template as a “live shortcut.” It lets you repeat the same piece of wiki all over the place, and whenever you edit that piece of wiki, it automatically updates everywhere. Let us know if further confusion remains.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:10, 7 September 2013 (PDT)

== Week 2 Feedback ==

* Thank you for submitting your assignment on time!
* Your translations were all correct; frame +3 does not contain an open reading frame, though.
* You will need to work on completing/correcting the links requested as part of the assignment. Specifically:
*# We have a specific naming convention that we would like you to use when naming your new individual journal pages. You should name them ''username week #''; for example your week 2 assignment page should be named ''Lena Week 2'', instead of "Genetic Code Assignment". You will need to '''''move''''' the contents of your "Genetic Code Assignment" page to your "Lena Week 2" page, for which you have a redlink on your user page. To do so, follow the directions listed [http://en.wikipedia.org/wiki/How_to_move_a_page here]]. We will be happy to talk you through this in class or office hours if you like. For the future, please make sure you are using the preferred naming convention for new pages.
*# You are missing the link from your User page to the [[Week 2 | Week 2 Assignment]] page.
*# You are missing the link from your individual week 2 journal entry back to your User page.
*# You need to add the category "Journal Entry" to your individual week 2 journal entry page. We are not actually using the category "Individual Homework" like Dr. Dionisio demo'd in class; we apologize for any confustion this caused.
*#* For the three items above, you can add these links to your template and then just use your template on your user page and all journal entry pages. That way, you won't forget to put the links in future assignments.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the corrections requested above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* Yes, the Nirenberg article was quite dense and written as a memoir as opposed to expository text.
* I have also answered your question on my user talk page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:59, 10 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making all requested corrections.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:57, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Good to hear that you succeeded in exerting control of your file extensions.
* You missed the '''cat''' command at the beginning of your reading frame answers. This is not a huge deal, but remember how attention to detail is a very important part of working with computers.
* Your '''sed''' and '''match''' skills are otherwise great! All of your commands were correct.
* Regarding the '''match''' question comparing it to '''grep'''/'''wc''', you missed reporting on how many of the matched pattern were found. For the third question, the distinction we were looking for is the way '''grep'''/'''wc''' can only count lines, thus missing cases where a pattern appears more than once in a single line.
* Your journal page was missing the requested ''Journal Entry'' category. Again falling under the “attention to detail” heading, please note the bulleted checklist provided under the assignment headings.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:50, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* ''-35 box was missed due to an extra slash in your '''sed''' command.''
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was incorrectly identified.''
* Ribosome binding site was correctly identified with an appropriate command.
* Your start codon was correctly identified with an appropriate command in the integrated all-in-one version, ''but is missing the added new line in the separate answer bullet.''
* ''Your stop codon command was never finalized.''
* The terminator was correctly identified with an appropriate command.
* ''Your mRNA strand is incorrect, and no command was supplied to show how you got your answer.''
* You determined the correct amino acid sequence ''but no command was supplied to show how you got your answer''.
In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:49, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* Missing Journal Entry category from Week 3 journal page has been added.

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:43, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was a thorough description of what you did. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:22, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, there were equal contributions from each student to this page.
* You need to link from the database wiki page to the [[Class Journal Week 5]] page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:19, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting everything on time!
* The wiki markup for movies-with-apostrophe query had the '''nowiki''' tags in the incorrect position—they should be completely surrounding the four apostrophes (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* Your last, individual query joins the ''member'' table, but that table is not actually necessary. When working with databases, we are sensitive to doing more work than necessary, because sometimes this additional work strongly detracts from speed, particularly if the tables contain large numbers of rows. An extra but unnecessary join will also, in some cases, change the results that you get back.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 11 October 2013 (PDT)

User talk:HDelgadi

2013-11-29T20:59:58Z

Dondi: Add week 9 feedback.

== Week 9 Feedback ==

Your week 9 work has (finally) been reviewed:
* Three out of the four file versions, as specified by the testing report template, are not listed.
* You logged all of the needed import/processing/export times.
* You successfully uploaded your .gdb file to the wiki.
* You successfully ran the Tally Engine.
* You successfully ran xmlpipedb-match.
* You successfully ran the appropriate PostgreSQL query.
* You successfully examined your .gdb file in Microsoft Access and compared its data against the benchmark version of the ''V. cholerae'' gene database.
* You correctly noted differences and similarities in the ID tallies from your various counts.
* You clearly indicated the ID pattern used for your ID searches/tallies.
* Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

== Week 8 Feedback ==

* I have reviewed your .xls and .txt files from part 1 of the Week 8 assignment. They are correct and ready to go for Tuesday. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:27, 14 October 2013 (PDT)''

== Week 1 Feedback ==

You did generally well for this first time out; do complete the wiki checklist and be consistent with summaries, as much as possible.

'''Items for completion/follow-up:'''
* Snail mail address
* Change summaries—try to enter these more consistently.
* Create a new wiki page
* Link to an external site
* Create a numbered list
* Comments inside the wiki markup
* Upload and link to an image
* Upload and link to a file
* Create and use a template
* Link to an assignment (Week ''n'') page
* Link to the shared journal from your user page
* Place your signature in the shared journal page

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:44, 3 September 2013 (PDT)

=== Week 1 Follow-Up ===

Thanks very much for completing your wiki checklist! Some notes on your latest work:
* You did the HHMI external link technically correctly, but notice how it appears as [http://cse.lmu.edu/programs/hhmi/] on your page. You can give this link some custom text by adding a space after the address, and putting the text after that space, [http://cse.lmu.edu/programs/hhmi/ like this] (edit this page to see how it was done).
* Your confusion about templates is noted (I saw that in your commented-out wiki markup!). You are creating it right; your confusion has to do with using it. Well, I’m using it down here:

(your template starts below)

{{HDelgadi}}

(your template just ended above)

:...note the curly braces (when you edit this page) and the removal of “Template:” That’s it! Whenever you write this into a wiki page, your template will show up there instead.

* Finally, you still have not “signed” your shared journal entries, but I know you can do the signature because you did it when you left a question on [[Talk:Dondi|my]] and [[Talk:Kdahlquist|Dr. Dahlquist’s]] talk pages. Make sure you do that on your shared journal entries too; it gives your reflection responses more of that “journal entry” feel.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:28, 7 September 2013 (PDT)

== Week 2 Journal Feedback ==

* Thank you for submitting your assignment on time.
* As noted in class, you had a couple of "point mutations" in frames +2 and +3.
* Remember to add the category "journal entry" to your individual journal page. If you add this category to your template and then use the template on your page, you will always remember to fulfill this part of your assignment.
* You have the opportunity to earn back the points you missed by making the corrections requested on the [[Week_3#Self-Correct_Week_2 | Week 3 Assignment]] page and the correction listed above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
* To answer your question about the Nirenberg reading, he was talking about the solubility of polyphenylalanine because he wanted to make sure that the product that was translated from the poly(U) was the same thing as a lab standard of polyphenylalanine. So he had to learn about that to make sure that they were the identical chemical.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:52, 10 September 2013 (PDT)''

P.S. I answered your question on my [[User talk:Kdahlquist|talk]] page. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:55, 10 September 2013 (PDT)''

=== Week 2 Follow-up ===

* Thank you for making the corrections to your translation.
* The category is still missing for this page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:56, 11 October 2013 (PDT)''

== Week 3 Feedback ==

* Thank you for submitting your assignment on time!
* Your experience with “Where’s my stuff” typically occurs when a computing system is strongly protecting file extensions like ''.txt'' and ''.html''. Different operating systems apply protections differently. Typically, there is a setting one can hit that tells the computer that you know what you are doing with respect to these extensions, after which you will then have greater control over these. In any case, nothing to worry about; what matters is that you got a sense for what role these file extensions play.
* Your '''sed''' and '''match''' skills are great! All of your commands were correct.
* Regarding the '''match''' question on "James," note that these look very much like names, so it is safe to guess that this search pattern may indicate a scientist or author (given the type of file you were searching).
* Your user page was missing a link to the [[Week 3]] assignment page. Strongly consider using a template for this, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:40, 14 September 2013 (PDT)

== Week 4 Feedback ==

Thank you for submitting your work on time! Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:
* -35 box was correctly identified with an appropriate command.
* -10 box was correctly identified with an appropriate command.
* ''Your transcription start site was off by one base.''
* Ribosome binding site was correctly identified with an appropriate command.
* Start codon was correctly identified with an appropriate command.
* Stop codon was correctly identified with an appropriate command.
* ''You missed that the terminator includes 4 additional base pairs after the hairpin.''
* ''Your mRNA strand is short—you only returned the start-to-stop codon, but transcription actually goes from the transcription start site to the end of the terminator.''
* You determined the correct amino acid sequence with an appropriate command.
In terms of your wiki link routine, everything was there except for:
* A link from your user page to the [[Week 4]] assignment.
Let me know if you have any questions.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:36, 24 September 2013 (PDT)

== Makeup Point Update ==

You have been credited for making the following change(s) to a wiki link checklist:
* A link from your user page to the Week 4 assignment was added

If you have any questions, let me know. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:40, 29 September 2013 (PDT)

== Week 5 Feedback ==

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

* Thank you for submitting your assignment on time.
* Your electronic lab notebook was a good description of what you did, but the formatting could be improved to be cleaner and easier to read. Starting again with the [[Week 8]] assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:23, 8 October 2013 (PDT)''

=== Week 5 Database Wiki ===

* Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, it appears that Mitchell was the main contributor to this page.
* I see that you used a template to move this page content to one with the proper name. There is a better way to move pages, see the drop down arrow next to the "View history" tab at the top of the page.
* Be careful about the formatting of your hyperlinks. Only use two square brackets when linking to internal wiki pages; external links use only single square brackets. Also, the numbering of your page with respect to the questions is off.
* You could have elaborated a bit more on your answers to the questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:22, 11 October 2013 (PDT)

== Week 6 Feedback ==

Thank you for submitting within your self-imposed extended deadline!
* The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the '''nowiki''' tag (like this: <nowiki>''''</nowiki> [view the wiki source to see how it’s done]).
* For the query requesting data on all movies, ratings, and members, you return more columns/fields than specifically requested. When working with databases, we are sensitive to doing more work than necessary, because sometimes this additional work strongly detracts from speed, particularly if the tables contain large numbers of rows.
* All your other database queries were correct and properly documented.
* You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:03, 11 October 2013 (PDT)

Main Page

2013-11-28T19:35:12Z

Dondi: /* Students */ Set final student roster.

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Downloading and Installing GenMAPP and MAPPFinder ===

* If you want to install GenMAPP and MAPPFinder on your own computer to use over the break, the instructions can be found on the [[Week_8#Downloading_and_installing_the_GenMAPP_and_MAPPFinder_Software | Week 8 Assignment]] page. Note that this software is Windows-only.

=== Grades Posted ===

* Grades for the [[Week 7]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. Hard copies of the corrected questions will be handed out in class on Tuesday, November 12.

=== Seminars and Events ===

=== Class Locations ===

* We will meet in ''lab'' for the remainder of the semester.
* Final presentations on Thursday, December 12 will take place in the ''classroom''.

== Group Projects ==

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

=== Teams ===

{| style="width: 75%"
| '''[[Chlamydia trachomatis | Team H(oo)KD]]'''
| '''[[Streptococcus pneumoniae | Team ATK]]'''
| '''[[Leishmania major | Off The Leish]]'''
| [[[[Team Name]]]]
|}

=== Guilds ===

{| style="width: 75%"
| [[Project Manager]]
| [[Coder]]
| [[Quality Assurance]]
| [[GenMAPP User]]
|}

=== Undergraduate Library Research Award ===

The projects for this course will qualify for the Hannon Library’s [http://digitalcommons.lmu.edu/ulra/ Undergraduate Library Research Award (ULRA)]. Click on the link if you are interested in this competition.


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 75%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
|
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma
* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Moody (2004) Chapter 6 (on MyLMU Connect]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]

[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]

| style="vertical-align: top; background: #eee" |Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class (MyLMU Connect)]
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

| style="vertical-align: top" | Introduction to relational databases
* Case study from one of the NAR databases: http://www.rhesusbase.org 
* Relating XML structure to relational structure

Test your understanding: http://xkcd.com/327/
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27 and 10/1)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations part 1
# Hilda - Mitchell
# Kurt - Kevin Meilak
# Tauras - Miles - Lena
# Lauren - Dillon

[[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Database presentations part 2
# Viktoria - Kevin McGee
# Katrina - Gabriel
# Stephen - Alina

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Campbell & Heyer Chapter 4 (on MyLMU Connect)]

| style="vertical-align: top" | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]

| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" | [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]

Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger et al. (2003) "MAPPFinder"
''Genome Biology'']]
| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Work session to complete DNA Microarray Analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']

[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
| style="vertical-align: top; background: #eee" |
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
* Groups assigned and species chosen
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guest speaker: Librarian Glenn Johnson-Grau
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Annotated bibliography of genomics papers for your species
** Select genome paper for journal club
** Select microarray paper
| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/12)

''Note different due date''

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

Main Page

2013-11-20T22:36:52Z

Dondi: /* Oral Presentations */ Correct oral presentation count.

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

== Grades Posted ==

* Grades for the [[Week 7]] assignment have been posted on the [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect grade center]. Hard copies of the corrected questions will be handed out in class on Tuesday, November 12.

=== Seminars and Events ===

* '''Biology Department Seminar:''' Thursday, November 21, 12:15 PM, SEA 200, Dr. Victor Carmona, LMU Biology, ''Chemical Ecology of Extrafloral Nectar Secretions from an Exotic Myrmecophyte''

=== Class Locations ===

* We will meet in ''lab'' for the remainder of the semester.

== Group Projects ==

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

=== Teams ===

{| style="width: 75%"
| '''[[Chlamydia trachomatis | Team H(oo)KD]]'''
| '''[[Streptococcus pneumoniae | Team ATK]]'''
| '''[[Leishmania major | Off The Leish]]'''
| [[[[Team Name]]]]
|}

=== Guilds ===

{| style="width: 75%"
| [[Project Manager]]
| [[Coder]]
| [[Quality Assurance]]
| [[GenMAPP User]]
|}

=== Undergraduate Library Research Award ===

The projects for this course will qualify for the Hannon Library’s [http://digitalcommons.lmu.edu/ulra/ Undergraduate Library Research Award (ULRA)]. Click on the link if you are interested in this competition.


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 75%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Kgosch | Kurt Gosch]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma
* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Moody (2004) Chapter 6 (on MyLMU Connect]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]

[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]

| style="vertical-align: top; background: #eee" |Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class (MyLMU Connect)]
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

| style="vertical-align: top" | Introduction to relational databases
* Case study from one of the NAR databases: http://www.rhesusbase.org 
* Relating XML structure to relational structure

Test your understanding: http://xkcd.com/327/
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27 and 10/1)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations part 1
# Hilda - Mitchell
# Kurt - Kevin Meilak
# Tauras - Miles - Lena
# Lauren - Dillon

[[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Database presentations part 2
# Viktoria - Kevin McGee
# Katrina - Gabriel
# Stephen - Alina

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Campbell & Heyer Chapter 4 (on MyLMU Connect)]

| style="vertical-align: top" | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]

| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" | [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]

Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger et al. (2003) "MAPPFinder"
''Genome Biology'']]
| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Work session to complete DNA Microarray Analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']

[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
| style="vertical-align: top; background: #eee" |
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
* Groups assigned and species chosen
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guest speaker: Librarian Glenn Johnson-Grau
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Annotated bibliography of genomics papers for your species
** Select genome paper for journal club
** Select microarray paper
| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/12)

''Note different due date''

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

Coder

2013-11-14T17:18:28Z

Dondi: /* Java Project Setup */ Add instructions on JDK.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* [[User:Gleis|Gabriel Leis]]: [[Leishmania_major|''Leishmania major'']]
* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|Team ATK ''Streptococcus pneumoniae'']]

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools: JDK 6 or 7 and [http://ant.apache.org ant]
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://www.oracle.com/technetwork/java/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 7u45''). Linux and Mac OS X computers typically already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://svn.code.sf.net/p/xmlpipedb/code then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://svn.code.sf.net/p/xmlpipedb/code should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Make sure that Eclipse is using a '''''JDK''''' (Java Development Kit) and not a ''JRE'' (Java Runtime Environment). To verify this, go to ''Window'' > ''Preferences'', click on ''Java'', click on ''Installed JREs'', and make sure that the checked environment has '''JDK''' in it. If not, you may need to add the environment (on Windows, it lives in <code>C:\Program Files\Java</code>) then check on it.
# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species; the portions that need to be customized are highlighted in asterisks.
public ***NameOfYourSpecies***UniProtSpeciesProfile() {
super("***Genus species***",
***taxonIDOfYourSpecies***,
"This profile customizes the GenMAPP Builder export for " +
"***Genus species***" +
" data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above. Again, the key information to customize is highlighted in asterisks.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "***species-specific-database-link***" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.



[[Category:Group Projects]]

Week 12

2013-11-12T17:04:48Z

Dondi: Week 12 update.

'''This journal entry is due on Friday, November 15, at midnight PST.''' ''(Thursday night/Friday morning)''

== Individual Journal Assignment ==

* From this week on, your Individual Journal Assignment will be to complete your electronic laboratory notebook that records your work on your team's final project.
** You need to record a narrative that describes all of the methods that you are using in enough detail so that the instructors or your other team members can follow and reproduce your work.
** Include links to artifacts you produce (files, images, testing reports, code, etc.)
* Store this journal entry as "''username'' Week 12" (i.e., this is the text to place between the square brackets when you link to this page). Alternately, you may wish to keep your narrative for Weeks 12, 13, and 14 on the same page so that all of your work is in one place, in which case, you could name it something like "''username'' Project Notebook".
* Link to this journal entry from your user page.
* Link back from your journal entry to your user page.
* In addition, link your journal entry to your team's home page and vice versa.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
* Add your team's category to your wiki page as well.

== Team Journal Assignment ==

* This week, the [[Project Manager]], in consultation with the rest of the team, will be setting intermediate milestones for the project deliverables to be completed by the journal deadline for the next three weeks.
* As a group, create a status report as to progress on each milestone that that you have set for the week.
* Store your status report in a shared "''Teamname'' Week 12 Status Report" page.
* Link to your status report from your team's home page and vice versa.
* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
* Add the "Journal Entry" category and your team's category to the end of the wiki page.

=== Reflection ===

Each team member should reflect on the team's progress:
# What were the week’s key accomplishments?
# What are next week’s target accomplishments?
# What team strengths were seen this week?
# What team weaknesses were seen this week?

[[Category:Assignment]]
[[Category: Group Projects]]

Week 11

2013-11-12T01:53:23Z

Dondi: Small spacing reformat.

'''This journal entry is due on Tuesday, November 12, at midnight PST.''' ''(Monday night/Tuesday morning) Note different due date.''

''A note on the grading for this assignment:''
* The individual journal entry containing the vocabulary definitions and article outline is worth a total of 10 points. Students will be graded on an individual basis for this portion of the assignment.
* The presentation is worth a total of 30 points; each member of the group will receive the same grade for this portion of the assignment.

{{Individual Journal Instructions|week=11}}


=== Preparation for Journal Club on Your Species ===

The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings is another). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research.

In preparation for the Journal Club on Tuesday, November 12, you will each individually complete the following assignment on your individual journal page.
# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own URL citation.'''''
# Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
#* What is the importance or significance of this work (i.e., your species)?
#* What were the methods used in the study?
#* Briefly state the result shown in each of the figures and tables.
#* How do the results of this study compare to the results of previous studies (See Discussion).
#* In addition to the journal article, please find and review the Model Organism Database (MOD) for your species. In particular, make sure to answer the following:
#*# What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
#*# What individual or organization maintains the database?
#*# What is their funding source(s)?
#*# Is there a license agreement or any restrictions on access to the database?
#*# How often is the database updated?
#*# Are there links to other databases?
#*# Can the information be downloaded?
#*#* In what file formats?
#*# Evaluate the “user-friendliness” of the database.
#*#* Is the Web site well-organized?
#*#* Does it have a help section or tutorial?
#*#* Run a sample query. Do the results make sense?
#*# What is the format (regular expression) of the main type of gene ID for this species? (for example, for ''Vibrio cholerae'' it was VC#### or VC_####).

=== Team Journal Club Presentation ===

Each group will prepare and give a 15 minute PowerPoint presentation for their species in class on Tuesday, November 12.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~15 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation.
** Specifically, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, November 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evalutated by the instructors using the [[Some_Topics_to_Consider_When_Critiquing_Talks | guidelines shown here]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What are the best points about the presentation's content, organization, clarity of visuals, and presentation style? Please give at least 2 specific examples.
*# What points need improvement? How would you improve them? Please give at least 2 specific examples.
* Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Team Journal Assignment ==

=== Team Wiki Pages ===

* Please make the requested changes to your team's wiki pages.
** The genome paper and the DNA microarray paper need to have the following information:
*** Full bibliographic reference according to [[Guidelines for Literature Citations in a Scientific Paper]]
*** Link to the HTML version of the full text on the publisher's web site.
*** Link to the PDF version (either uploaded to this wiki if no copyright restrictions or a link to the publisher download site).
** Please "comment out" the microarray papers that you won't be using for the project.
* Add additional navigation links to your team's pages using a template for your team.
** Links to individual user pages for the team members.
** Links to the [[Gene Database Project]] main page and [[Gene Database Project Report Guidelines]] page.
** Links to the guild pages.
** Links to any subpages your team creates.
** Add the category "Group Projects" in addition to your individual team category.
* Be sure to name your team something other than your species name.

[[Category: Group Projects]]

Week 11

2013-11-12T01:52:39Z

Dondi: /* Preparation for Journal Club on Your Species */ Date update (better late than never).

'''This journal entry is due on Tuesday, November 12, at midnight PST.''' ''(Monday night/Tuesday morning) Note different due date.''

''A note on the grading for this assignment:''
* The individual journal entry containing the vocabulary definitions and article outline is worth a total of 10 points. Students will be graded on an individual basis for this portion of the assignment.
* The presentation is worth a total of 30 points; each member of the group will receive the same grade for this portion of the assignment.

{{Individual Journal Instructions|week=11}}



=== Preparation for Journal Club on Your Species ===

The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings is another). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research.

In preparation for the Journal Club on Tuesday, November 12, you will each individually complete the following assignment on your individual journal page.
# Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. '''''Each definition must have it's own URL citation.'''''
# Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
#* What is the importance or significance of this work (i.e., your species)?
#* What were the methods used in the study?
#* Briefly state the result shown in each of the figures and tables.
#* How do the results of this study compare to the results of previous studies (See Discussion).
#* In addition to the journal article, please find and review the Model Organism Database (MOD) for your species. In particular, make sure to answer the following:
#*# What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
#*# What individual or organization maintains the database?
#*# What is their funding source(s)?
#*# Is there a license agreement or any restrictions on access to the database?
#*# How often is the database updated?
#*# Are there links to other databases?
#*# Can the information be downloaded?
#*#* In what file formats?
#*# Evaluate the “user-friendliness” of the database.
#*#* Is the Web site well-organized?
#*#* Does it have a help section or tutorial?
#*#* Run a sample query. Do the results make sense?
#*# What is the format (regular expression) of the main type of gene ID for this species? (for example, for ''Vibrio cholerae'' it was VC#### or VC_####).

=== Team Journal Club Presentation ===

Each group will prepare and give a 15 minute PowerPoint presentation for their species in class on Tuesday, November 12.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~15 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation.
** Specifically, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, November 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evalutated by the instructors using the [[Some_Topics_to_Consider_When_Critiquing_Talks | guidelines shown here]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What are the best points about the presentation's content, organization, clarity of visuals, and presentation style? Please give at least 2 specific examples.
*# What points need improvement? How would you improve them? Please give at least 2 specific examples.
* Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Team Journal Assignment ==

=== Team Wiki Pages ===

* Please make the requested changes to your team's wiki pages.
** The genome paper and the DNA microarray paper need to have the following information:
*** Full bibliographic reference according to [[Guidelines for Literature Citations in a Scientific Paper]]
*** Link to the HTML version of the full text on the publisher's web site.
*** Link to the PDF version (either uploaded to this wiki if no copyright restrictions or a link to the publisher download site).
** Please "comment out" the microarray papers that you won't be using for the project.
* Add additional navigation links to your team's pages using a template for your team.
** Links to individual user pages for the team members.
** Links to the [[Gene Database Project]] main page and [[Gene Database Project Report Guidelines]] page.
** Links to the guild pages.
** Links to any subpages your team creates.
** Add the category "Group Projects" in addition to your individual team category.
* Be sure to name your team something other than your species name.

[[Category: Group Projects]]

Coder

2013-11-05T18:42:32Z

Dondi: /* Initial Code Checkout */ Update SourceForge SVN repository.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* [[User:Gleis|Gabriel Leis]]: [[Leishmania_major|''Leishmania major'']]
* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|Team ATK ''Streptococcus pneumoniae'']]

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools: JDK 6 or 7 and [http://ant.apache.org ant]
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://www.oracle.com/technetwork/java/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 7u45''). Linux and Mac OS X computers typically already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://svn.code.sf.net/p/xmlpipedb/code then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://svn.code.sf.net/p/xmlpipedb/code should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species; the portions that need to be customized are highlighted in asterisks.
public ***NameOfYourSpecies***UniProtSpeciesProfile() {
super("***Genus species***",
***taxonIDOfYourSpecies***,
"This profile customizes the GenMAPP Builder export for " +
"***Genus species***" +
" data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above. Again, the key information to customize is highlighted in asterisks.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "***species-specific-database-link***" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.

==GenMAPP Beta Release Zip==
[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]

[[Category:Group Projects]]

Coder

2013-11-05T17:52:06Z

Dondi: /* Customize the Species Profile */ More asterisks.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* [[User:Gleis|Gabriel Leis]]: [[Leishmania_major|''Leishmania major'']]
* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|''Streptococcus pneumoniae'']]

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools: JDK 6 or 7 and [http://ant.apache.org ant]
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://www.oracle.com/technetwork/java/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 7u45''). Linux and Mac OS X computers typically already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species; the portions that need to be customized are highlighted in asterisks.
public ***NameOfYourSpecies***UniProtSpeciesProfile() {
super("***Genus species***",
***taxonIDOfYourSpecies***,
"This profile customizes the GenMAPP Builder export for " +
"***Genus species***" +
" data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above. Again, the key information to customize is highlighted in asterisks.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "***species-specific-database-link***" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.

==GenMAPP Beta Release Zip==
[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]

[[Category:Group Projects]]

Coder

2013-11-05T17:45:40Z

Dondi: /* Customize the Species Profile */ Update starter species profile class declaration.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* [[User:Gleis|Gabriel Leis]]: [[Leishmania_major|''Leishmania major'']]
* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|''Streptococcus pneumoniae'']]

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools: JDK 6 or 7 and [http://ant.apache.org ant]
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://www.oracle.com/technetwork/java/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 7u45''). Linux and Mac OS X computers typically already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species; the portions that need to be customized are highlighted in asterisks.
public ***NameOfYourSpecies***UniProtSpeciesProfile() {
super("***Genus species***",
***taxonIDOfYourSpecies***,
"This profile customizes the GenMAPP Builder export for " +
"***Genus species***" +
" data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "species-specific-database-link" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.

==GenMAPP Beta Release Zip==
[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]

[[Category:Group Projects]]

Coder

2013-11-05T17:00:45Z

Dondi: /* Software to Install */ Version number update.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* [[User:Gleis|Gabriel Leis]]: [[Leishmania_major|''Leishmania major'']]
* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|''Streptococcus pneumoniae'']]

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools: JDK 6 or 7 and [http://ant.apache.org ant]
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://www.oracle.com/technetwork/java/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 7u45''). Linux and Mac OS X computers typically already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species.
public NameOfYourSpeciesUniProtSpeciesProfile() {
super("Genus species",
"This profile customizes the GenMAPP Builder export for Genus species data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "species-specific-database-link" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.

==GenMAPP Beta Release Zip==
[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]

[[Category:Group Projects]]

Coder

2013-11-05T16:46:35Z

Dondi: /* Guild Members */ Add coders and their respective teams.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* [[User:Gleis|Gabriel Leis]]: [[Leishmania_major|''Leishmania major'']]
* [[User:Mpetredi|Mitchell Petredis]]: [[Sinorhizobium_meliloti|''Sinorhizobium meliloti'']]
* [[User:Ksherbina|Katrina Sherbina]]: [[Chlamydia_trachomatis|Team H(oo)KD, ''Chlamydia trachomatis'']]
* [[User:Taur.vil|Tauras Vilgalys]]: [[Streptococcus_pneumoniae|''Streptococcus pneumoniae'']]

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools: JDK 6 or 7 and [http://ant.apache.org ant]
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://java.sun.com/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 6 Update 22''). Linux and Mac OS X computers already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species.
public NameOfYourSpeciesUniProtSpeciesProfile() {
super("Genus species",
"This profile customizes the GenMAPP Builder export for Genus species data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "species-specific-database-link" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.

==GenMAPP Beta Release Zip==
[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]

[[Category:Group Projects]]

Coder

2013-11-05T06:37:47Z

Dondi: /* Milestone 1 */ A few more requirements tweaks.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* ''To be determined.''

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools: JDK 6 or 7 and [http://ant.apache.org ant]
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://java.sun.com/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 6 Update 22''). Linux and Mac OS X computers already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species.
public NameOfYourSpeciesUniProtSpeciesProfile() {
super("Genus species",
"This profile customizes the GenMAPP Builder export for Genus species data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "species-specific-database-link" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.

==GenMAPP Beta Release Zip==
[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]

[[Category:Group Projects]]

Coder

2013-11-05T06:36:42Z

Dondi: /* Milestone 1 */ Update some version numbers and nomenclature.

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

== Guild Members ==

* ''To be determined.''

== Milestones ==

=== Milestone 1 ===

# Set up the working environment
#* PostgreSQL on Windows (http://www.postgresql.org)
#* GenMAPP Builder (http://sourceforge.net/projects/xmlpipedb)
#** Current version is gmbuilder2.0-b71
#** Requires Java 6 or 7 runtime environment
#*** Note that you need to use 32-bit Java
#* GenMAPP (http://genmapp.org)
#* XMLPipeDB ''match'' utility for counting IDs in XML files
#* Microsoft Access or any other tool that can read .mdb files
# Set up the development environment
#* Java developer tools
#* Subversion (for checking code in/out of SourceForge)
#* One or more members in group need to get Java running
#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Keck lab Windows machines
#* XMLPipeDB Match utility
#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used
# (with QA) Get a full import-export cycle done.
# (with QA) Decide on a file/version management scheme/system.
# Document/log all work done, problems encountered, and how they were resolved.

=== Milestone 2 ===

# Get a SourceForge account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project.
#* Once you are set up as a developer, you can download the GenMAPP Builder source code.
#* You can then use ''ant'' to build your own copy of GenMAPP Builder from scratch.
#* As needed, coders should arrange for a walkthrough or other help session with Dr. Dionisio.
# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.

=== Milestone 3 ===

# Add a ''species profile'' to the GenMAPP Builder code base.
# Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
# Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
#* The URL would need to be determined first, of course.
# Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species.
# (probably more like milestone 4 than 3) Implement this export behavior.
# When ready, commit your species profile to SourceForge and release a new version of GenMAPP Builder.

== GenMAPP Builder Project Setup and Initial Build ==

This section of the page seeks to provide a guide for building new versions of GenMAPP Builder.

While there are many ways to update and maintain GenMAPP Builder code, for uniformity these instructions will assume the use of [http://www.eclipse.org Eclipse] for viewing, modifying, and updating GenMAPP Builder. The main benefit of Eclipse is that it is largely a one-stop shop for performing all of these tasks.

The instructions listed in this [[#Setup|Setup]] section need only be performed once. Once done correctly, you will primarily be doing what is described in the [[#Common Tasks|Common Tasks]] section.

=== Software to Install ===

# While you can only ''run'' GenMAPP Builder on Windows, you can ''build'' it from any platform: Windows, Linux, or Mac OS X. If you are using Windows, you need to download and install the Java Development Kit from http://java.sun.com/javase/downloads. You will want the ''Java Platform, Standard Edition '''JDK''''' (which, at this writing, is ''JDK 6 Update 22''). Linux and Mac OS X computers already come with JDK included.
# Download and install Eclipse from its [http://www.eclipse.org/downloads download web site]. Either '''Eclipse IDE for Java Developers''' or '''Eclipse IDE for Java EE Developers''' will work.
# Download and install the Subclipse plug-in for Eclipse (this is the software that is needed for accessing the source code in SourceForge). Instructions for downloading and installing Subclipse can be found on the [http://subclipse.tigris.org Subclipse home page].


=== Initial Code Checkout ===

# Get an account from http://sourceforge.net and send your account name to Dr. Dionisio, for inclusion as an XMLPipeDB developer.
# Run Eclipse.
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''. If you don't see this, double-check your installation of Subclipse.
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
# Set the URL to https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb then click ''Finish''.
#* Remember to accept the security certificate for the SVN repository
# https://xmlpipedb.svn.sourceforge.net/svnroot/xmlpipedb should now appear in the list. Double-click on it to see its contents.
# Double-click on ''trunk''.
# Right-click on ''gmbuilder'' and choose ''Checkout...''.
# Choose ''Check out as a project configured using the New Project Wizard'' then click ''FInish''.
# If you are asked for a username and password, enter your SourceForge username and password.
# In the ''New Project'' dialog that opens, choose ''Java Project'' from the list.
# Click ''Next > ''.
# You may enter any ''Project name:'' that you like. ''gmbuilder'' or ''xmlpipedb-gmbuilder'' isn’t bad, for example.
# Click ''Finish''. You should end up in the ''Java'' perspective, with your project appearing as a top-level folder in the ''Package Explorer'' tab.

=== Java Project Setup ===

# Upon a successful checkout, you should have a ''gmbuilder'' Java project in Eclipse. Make sure that you are in the ''Java'' perspective by choosing ''Window'' > ''Open Perspective'' > ''Java'' (or choosing ''Java'' from ''Other...'' if ''Java'' is not already in the ''Open Perspective'' submenu).
# Double-click on the ''gmbuilder'' folder (or whatever you called it) to view its contents.
# Double-click on the ''lib'' folder.
# Shift-click and select all files in the ''lib'' folder and then control-click (or, on a Mac, Command-click) on every file inside the ''lib'' folder whose name does not end in ''.jar''.
# Once all of these files are selected, right-click on one of them and choose ''Build Path'' > ''Add to Build Path'' from the popup menu that comes up.
# The ''src'' folder should look different from the other folders in that it has a little brown square badge on its upper-right corner. If not, right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# Do the same to the ''test'' folder: right-click on it and choose ''Build Path'' > ''Use as Source Folder'' from the popup menu that comes up.
# If you see any red ''x'' icons appear, something has not been set up right. Contact other guild members or Dr. Dionisio for troubleshooting if you get stuck.

== Adding a Species Profile to GenMAPP Builder ==

All of this work happens in the ''Java'' perspective, so switch to that first if you’re not already there.

=== Create the Species Profile ===

# Expose the contents of the ''src'' folder.
# Right-click on the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package and choose ''New > Class'' from the popup menu.
# In the dialog that appears, enter the following:
#* '''Name:''' ''name-of-your-species-without-spaces''UniProtSpeciesProfile (no spaces, capitalizing the first letters of each word)
#* '''Superclass:''' edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile (you can also click on ''Browse...'' to navigate to this if you don’t feel like typing)
# Click ''Finish''. There should now be a new ''.java'' file within the ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'' package (the one you just created).

=== Customize the Species Profile ===

* Open the file that you have just created. It should appear in the editor area of Eclipse.
* Override the method that supplies the name of the species and the description of the profile: add the following constructor block right below the ''public class'' line in the new file. Remember to customize according to your particular species.
public NameOfYourSpeciesUniProtSpeciesProfile() {
super("Genus species",
"This profile customizes the GenMAPP Builder export for Genus species data loaded from a UniProt XML file.");
}
* To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, add the following method block right below the constructor block that you added above.
@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Species", "|" + getSpeciesName() + "|" }
});

tableManager.submit("Systems", QueryType.update, new String[][] {
{ "SystemCode", "N" },
{ "Link", "species-specific-database-link" }
});

return tableManager;
}
* Note the '''species-specific-database-link''' placeholder above. This is a species-specific URL that returns a web page describing a gene for that species. It should look like a standard URL, with the tilde ('''~''') standing in for the gene ID. For example, the link for ''Vibrio cholerae'' is <code>http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~</code>. The link for ''Plasmodium falciparum'' is <code>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=PlasmoDB&source_id=~</code>. Work with your GenMAPP User and/or QA to determine the appropriate URL for your species.
* Your code may have a red error badge at this point; assuming you typed everything in exactly, the fix for this is to choose ''Organize Imports'' from the ''Source'' menu. If the red error badge persists, make sure that you typed everything in correctly.
* Save the file and see if these changes worked (see below).

Additional customization, particularly with regard to the exported data, will depend on the species. Communicate with your QA to see if additional customization is needed. If the additional customization is not too complicated, you might be able to do the work yourself with some instructions. However, if the customization is too difficult, Dr. Dionisio will probably be the one to do the work.

=== Customize the IDs that the Tally Engine Counts ===

This step is technically optional, in that it does not affect the overall import/export process. However, it ''does'' help you to get an idea of how well the IDs from the UniProt XML file are being brought into the relational database.

# First, determine which IDs (outside of the defaults that the tally engine already counts) you would like to count. At a minimum, this includes at least the ''ordered locus'' IDs from the ''gene/name'' tag in the UniProt XML file. There may be more; consult with your QA.
# For each of these IDs, determine the following:
#* Where in the XML file they can be found, in terms of which XML tags
#* Where in the relational database they can be found, in terms of which relational tables
# Under ''edu.lmu.xmlpipedb.gmbuilder.resource.properties'', open ''gmbuilder.properties''.
# Locate the block of text below (it’s near the bottom). You will insert the customizations that will be described right above this block.
#
# wizard.properties
#

* First, mark out the section that denotes the customization for your species:
# Species name
* Next, rewrite your species name without spaces and all lowercase (e.g., ''Plasmodium falciparum'' becomes ''plasmodiumfalciparum''). Specify the number of additional custom IDs to count as follows, where ''speciesname'' is your no-space, all-lowercase species name, and ''#'' represents the actual number of IDs:
speciesname_level_amount=#
* Now, ''for each custom ID'', you need to specify three things: an ''element'', a ''query'', and a ''name''. Each of these items is numbered, starting from 0. Each item number is called a ''level''.
*# The ''element'' states where you expect an ID to be found in the UniProt XML file. It starts with ''uniprot/entry'', then continues with additional tags as needed. After the tag, you may specify, separated by ampersands (''&''s), any specific attributes that you would like to choose.
*# The ''query'' states the SQL query that you would use to count the IDs in the relational database. The query would be exactly as you would type it if you were entering it directly into the relational database.
*# The ''name'' is a simple label: this is how you would like to identify this ID in the final Tally Engine table.
* You can write these in any order, though existing customizations group them by ''element'', ''query'', and ''name''. For example, if your species is ''speciesname'' and you only need to count ordered locus IDs, you would add:
# Species name
speciesname_level_amount=1

speciesname_element_level0=uniprot/entry/gene/name&type&ordered locus

speciesname_query_level0=select count(*) from genenametype where type = 'ordered locus';

speciesname_query_level0=Ordered Locus
* Note how the ''element'' ends with ''name&type&ordered locus'', because the ''name'' tag in the UniProt XML file will have different types (e.g., “primary”, “ORF”, “synonym”, “ordered locus”, etc.). For ''ordered locus'' IDs, we only want to count the ''name'' IDs whose type is “ordered locus”.

Once you are done with these customizations, you can test your work by building a new version of GenMAPP Builder, connecting to a relational database that already has imported data (or importing data first if needed), then running the Tally Engine. The resulting table should include, in addition to the defaults that you have seen before, the new IDs that you have added.

=== Add the Species Profile to the Catalog of Known Species Profiles ===

The last step involves actually making GenMAPP Builder ''know'' that your new species profile exists. This involves a change in an existing file:
* Under ''edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles'', open ''UniProtDatabaseProfile.java''.
* Near the top of the file is a block that looks like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile() });
* What you want to do is add the species profile that you just created to this block. If your species profile is called ''MySpecialUniProtSpeciesProfile'', your modified code should look like this:
super("org.uniprot.uniprot.Uniprot",
"This profile defines the requirements "
+ "for any UniProt centric gene database.",
new SpeciesProfile[] {
new EscherichiaColiUniProtSpeciesProfile(),
new ArabidopsisThalianaUniProtSpeciesProfile(),
new PlasmodiumFalciparumUniProtSpeciesProfile(),
new VibrioCholeraeUniprotSpeciesProfile(),
new MySpecialUniProtSpeciesProfile() });
* Essentially, you need to add an item to the comma-separated list, beginning with ''new'', followed by the species profile name, finally followed by ''()''.
* Save your changes, do ''Organize Imports'' to eliminate any red errors, and try a test build!

=== Build, Test, and Possibly Commit ===

# Create a new distribution of GenMAPP Builder based on [[#Creating a Distribution|Creating a Distribution]].
# Perform a new export run with this version of GenMAPP Builder (you can skip the import steps and use the same PostgreSQL database if it’s available).
# Check the ''Systems'' table in the resulting ''.gdb'' to see if it contains the custom information:
#* Open the ''.gdb'' in Microsoft Access, then open the ''Systems'' table.
#* Look for the record for ''OrderedLocusNames''. Your species name should appear under the ''Species'' column and your link URL should appear under the ''Link'' column.
# If all goes well, commit your code as described in [[#Updating and Committing Code|Updating and Committing Code]]. You have now officially contributed to the XMLPipeDB project ''':)'''

== Common Tasks ==

The tasks in this section reflect the typical development cycle.

==== Updating and Committing Code ====

# Right-click on the ''gmbuilder'' project folder and choose ''Team Synchronize...'' from the popup menu.
# You will be switched to the ''Team Synchronization'' perspective.
# The presence of blue-arrowed files means that the server has new updates for you to download. Right-click on the ''gmbuilder'' project folder and choose ''Update'' from the popup menu.
# It is good “developer etiquette” to build a new distribution from scratch when you’ve received updates prior to committing your own changes. Thus, after the update, return to the ''Java'' perspective, do a ''build.xml'' > ''clean'' followed by a ''build.xml'' > ''dist''.
# If everything works out, do ''Team Synchronize...'' again. If there are new updates (in the tiny amount of time since you last updated!), test things again.
# Eventually, you will see a ''Team Synchronize...'' with no incoming code. At this point, go ahead and commit the gray-arrowed files by right-clicking on them and choosing ''Commit...''.
# Just like with the wiki, it is good developer etiquette to describe briefly the nature of the changes that you are committing.
# Even if you have nothing to commit, it is still a good idea to invoke ''Team Synchronize...'' regularly so that you are kept up-to-date with regard to files that others may be committing.

==== Creating a Distribution ====

To create your own version of GenMAPP Builder based on the code you have in Eclipse (which may contain some new changes/customizations that you would like to test), follow these steps:

# Switch to Eclipse’s Java perspective.
# Within the ''gmbuilder'' Java project is a file called ''build.xml''. It should have an icon that appears to include an ant.
# Right click on ''build.xml'' and choose ''Run As'' > ''Ant Build...'' (the one with the ellipses) from the popup menu that appears.
# In the ''Edit Configuration'' dialog that appears, check on the ''clean'' and ''dist'' items in the ''Targets'' tab. The ''Target execution order'' section near the bottom of the dialog should say ''clean, dist''.
# Click the ''Run'' button. The computer will work for a bit.
# When it is done, right-click on the ''gmbuilder'' project folder and choose ''Refresh'' (''F5'' is its keyboard shortcut).
# You should see a ''dist'' folder appear inside the ''gmbuilder'' project folder.
# This is your personally-built copy of ''GenMAPP Builder''. Its contents correspond to the extracted contents of the ''gmbuilder-2.0b59.zip'' file that was downloaded in class.
# Run ''pgAdmin III'' and start a database, then run this copy of ''GenMAPP Builder'' as you would the “released” copy. The program should behave just like the one that you downloaded and have been using.

==== Releasing to SourceForge ====

# Build a new version of GenMAPP Builder (''ant dist'').
# Rename the ''dist'' folder as ''gmbuilder-2.0b##'' where ''##'' is the next available version number.
# Compress the ''gmbuilder-2.0b##'' folder as a ''.zip'' file.
# Login to SourceForge.
# Go to the ''xmlpipedb'' project site.
# Go to file releases.
# Create a folder for the new release.
# Upload the ''.zip'' into the folder.
# Upload the release notes.
# Mark the release notes as belonging to the .zip.
# Mark the current release as the default Windows download by selecting the small i button next to .zip.

==GenMAPP Beta Release Zip==
[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]

[[Category:Group Projects]]

User:Kdahlquist

2013-10-31T19:15:37Z

Dondi: /* UniProt XML */ Add V. cholerae download link.

== Kam D. Dahlquist, Ph.D. ==

=== Contact Information ===

Associate Professor
Department of Biology
Loyola Marymount University
1 LMU Drive, MS 8220
Los Angeles, CA 90045-2659
Tel: 310-338-7697
Fax: 310-338-4479
E-mail: kdahlquist at lmu dot edu
Office: Seaver 218
Lab: Seaver 222

'''Office Hours (Fall 2013):''' Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment

For more information about me, please see my web pages:
* [http://myweb.lmu.edu/kdahlqui http://myweb.lmu.edu/kdahlqui]
* [http://www.openwetware.org/wiki/User:Kam_D._Dahlquist My User Page at OpenWetware.org]

=== Education ===

* '''Ph.D., University of California, Santa Cruz''', Molecular, Cellular, and Developmental Biology Program, March 2000
* '''B.A., Pomona College''', Claremont, California, Biology, ''cum laude'', May 1993
* '''Study Abroad Program, University College, Oxford University''', Oxford, England, Specialized tutorial in Philosophy of Science, Fall 1991

=== Work Experience ===

* Affiliate Faculty, Bioethics Institute, Loyola Marymount University, Los Angeles, California, 2013-present
* William F. McLaughlin Chair of Biology, 2010–2012
* Associate Professor, Department of Biology, Loyola Marymount University, Los Angeles, California, 2009–present
* Assistant Professor, Department of Biology, Loyola Marymount University, Los Angeles, California, 2005–2009,
* Assistant Professor, Department of Biology, Vassar College, Poughkeepsie, New York, 2003–2005
* Postdoctoral Fellow, Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, 2000–2003
* Adjunct Lecturer, Department of Biology, Santa Clara University, Santa Clara, California, Spring 2000
* Visiting Researcher, Department of Structural Biology, Stanford University, Stanford, California, 1997–2000
* Research Assistant, Department of Biology, University of California, Santa Cruz, California, 1994–1997

=== Personal Interests and Hobbies ===

* Reading science fiction
* Dance
* Needlework
* Cooking and baking

=== Gene Database Source Files ===

==== GO ====

* [[Media:Go daily-termdb-20131021-125457pm.zip | OBO XML .zip file]]
** Creation date of unzipped file: 2013-10-21 12:54:57 pm

==== UniProt XML ====

From UniProt release 2013_10 - October 16, 2013

* ''Arabidopsis thaliana''
** Tax ID: 3702
** [[Media:Arabidopsis_thaliana_UniProt_20131031.xml.gz | Arabidopsis_thaliana_UniProt_20131031.xml.gz]]
* ''Escherichia coli''
** Tax ID: 83333 (includes MG1655 Tax ID 511145 and W3110 Tax ID 316407)
** [[Media:Escherichia_coli_UniProt_20131031.xml.gz | Escherichia_coli_UniProt_20131031.xml.gz]]
* ''Helicobacter pylori'' (strain ATCC 700392 / 26695) (Campylobacter pylori)
** Tax ID: 85962
** [[Media:Helicobacter_pylori_UniProt_20131029.xml.gz | Helicobacter_pylori_UniProt_20131029.xml.gz]]
* ''Mycobacterium smegmatis''
** Tax ID 246196
** [[Media:Mycobacterium_smegmatis_UniProt_20131029.xml.gz | Mycobacterium_smegmatis_UniProt_20131029.xml.gz]]
* ''Mycobacterium tuberculosis''
** Tax ID 83332; looks like ID has changed to 1773
** [[Media:Mycobacterium_tuberculosis_UniProt_20131031.xml.gz | Mycobacterium_tuberculosis_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a1773+keyword%3a1185&format=*&compress=yes Download page]
* ''Plasmodium falciparum''
** Tax ID 36329
** [[Media:Plasmodium_falciparum_UniProt_20131031.xml.gz | Plasmodium_falciparum_UniProt_20131031.xml.gz]]
* ''Pseudomonas aerugenosa''
** Tax ID 208964
**[[Media:Pseudomonas_aerugenosa_UniProt_20131031.xml.gz | Pseudomonas_aerugenosa_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&format=*&compress=yes Download page]
* ''Salmonella typhimurium''
** Tax ID 99287
** [[Media:Salmonella_typhimurium_UniProt_20131031.xml.gz | Salmonella_typhimurium_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a99287+keyword%3a1185&format=*&compress=yes Download page]
* ''Staphylococcus aureus''
** Tax ID 282458
** [[Media:Staphylococcus_aureus_UniProt_20131031.xml.gz | Staphylococcus_aureus_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a282458+keyword%3a181&format=*&compress=yes Download page]
* ''Vibrio cholerae''
** Tax ID 243277
** [[Media:46.V cholerae ATCC 39315-20131021.xml.zip | 46.V cholerae ATCC 39315-20131021.xml.zip]]
*** [http://www.uniprot.org/uniprot/?query=organism:243277+keyword:1185 Download page]

==== GOA ====

* ''Vibrio cholerae''
** [[Media:46.V cholerae ATCC 39315-20131021.goa.zip | 46.V cholerae ATCC 39315-20131021.goa.zip]]

User:Kdahlquist

2013-10-31T19:14:09Z

Dondi: /* Gene Database Source Files */ Initial uploads for V. cholerae (though filenames diverge from the others).

== Kam D. Dahlquist, Ph.D. ==

=== Contact Information ===

Associate Professor
Department of Biology
Loyola Marymount University
1 LMU Drive, MS 8220
Los Angeles, CA 90045-2659
Tel: 310-338-7697
Fax: 310-338-4479
E-mail: kdahlquist at lmu dot edu
Office: Seaver 218
Lab: Seaver 222

'''Office Hours (Fall 2013):''' Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment

For more information about me, please see my web pages:
* [http://myweb.lmu.edu/kdahlqui http://myweb.lmu.edu/kdahlqui]
* [http://www.openwetware.org/wiki/User:Kam_D._Dahlquist My User Page at OpenWetware.org]

=== Education ===

* '''Ph.D., University of California, Santa Cruz''', Molecular, Cellular, and Developmental Biology Program, March 2000
* '''B.A., Pomona College''', Claremont, California, Biology, ''cum laude'', May 1993
* '''Study Abroad Program, University College, Oxford University''', Oxford, England, Specialized tutorial in Philosophy of Science, Fall 1991

=== Work Experience ===

* Affiliate Faculty, Bioethics Institute, Loyola Marymount University, Los Angeles, California, 2013-present
* William F. McLaughlin Chair of Biology, 2010–2012
* Associate Professor, Department of Biology, Loyola Marymount University, Los Angeles, California, 2009–present
* Assistant Professor, Department of Biology, Loyola Marymount University, Los Angeles, California, 2005–2009,
* Assistant Professor, Department of Biology, Vassar College, Poughkeepsie, New York, 2003–2005
* Postdoctoral Fellow, Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, 2000–2003
* Adjunct Lecturer, Department of Biology, Santa Clara University, Santa Clara, California, Spring 2000
* Visiting Researcher, Department of Structural Biology, Stanford University, Stanford, California, 1997–2000
* Research Assistant, Department of Biology, University of California, Santa Cruz, California, 1994–1997

=== Personal Interests and Hobbies ===

* Reading science fiction
* Dance
* Needlework
* Cooking and baking

=== Gene Database Source Files ===

==== GO ====

* [[Media:Go daily-termdb-20131021-125457pm.zip | OBO XML .zip file]]
** Creation date of unzipped file: 2013-10-21 12:54:57 pm

==== UniProt XML ====

From UniProt release 2013_10 - October 16, 2013

* ''Arabidopsis thaliana''
** Tax ID: 3702
** [[Media:Arabidopsis_thaliana_UniProt_20131031.xml.gz | Arabidopsis_thaliana_UniProt_20131031.xml.gz]]
* ''Escherichia coli''
** Tax ID: 83333 (includes MG1655 Tax ID 511145 and W3110 Tax ID 316407)
** [[Media:Escherichia_coli_UniProt_20131031.xml.gz | Escherichia_coli_UniProt_20131031.xml.gz]]
* ''Helicobacter pylori'' (strain ATCC 700392 / 26695) (Campylobacter pylori)
** Tax ID: 85962
** [[Media:Helicobacter_pylori_UniProt_20131029.xml.gz | Helicobacter_pylori_UniProt_20131029.xml.gz]]
* ''Mycobacterium smegmatis''
** Tax ID 246196
** [[Media:Mycobacterium_smegmatis_UniProt_20131029.xml.gz | Mycobacterium_smegmatis_UniProt_20131029.xml.gz]]
* ''Mycobacterium tuberculosis''
** Tax ID 83332; looks like ID has changed to 1773
** [[Media:Mycobacterium_tuberculosis_UniProt_20131031.xml.gz | Mycobacterium_tuberculosis_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a1773+keyword%3a1185&format=*&compress=yes Download page]
* ''Plasmodium falciparum''
** Tax ID 36329
** [[Media:Plasmodium_falciparum_UniProt_20131031.xml.gz | Plasmodium_falciparum_UniProt_20131031.xml.gz]]
* ''Pseudomonas aerugenosa''
** Tax ID 208964
**[[Media:Pseudomonas_aerugenosa_UniProt_20131031.xml.gz | Pseudomonas_aerugenosa_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&format=*&compress=yes Download page]
* ''Salmonella typhimurium''
** Tax ID 99287
** [[Media:Salmonella_typhimurium_UniProt_20131031.xml.gz | Salmonella_typhimurium_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a99287+keyword%3a1185&format=*&compress=yes Download page]
* ''Staphylococcus aureus''
** Tax ID 282458
** [[Media:Staphylococcus_aureus_UniProt_20131031.xml.gz | Staphylococcus_aureus_UniProt_20131031.xml.gz]]
*** [http://www.uniprot.org/uniprot/?query=organism%3a282458+keyword%3a181&format=*&compress=yes Download page]
* ''Vibrio cholerae''
** Tax ID 243277
** [[Media:46.V cholerae ATCC 39315-20131021.xml.zip | 46.V cholerae ATCC 39315-20131021.xml.zip]]

==== GOA ====

* ''Vibrio cholerae''
** [[Media:46.V cholerae ATCC 39315-20131021.goa.zip | 46.V cholerae ATCC 39315-20131021.goa.zip]]

File:46.V cholerae ATCC 39315-20131021.goa.zip

2013-10-31T19:12:00Z

Dondi: GOA V. cholerae 10/21/2013

GOA V. cholerae 10/21/2013

File:46.V cholerae ATCC 39315-20131021.xml.zip

2013-10-31T19:11:38Z

Dondi: UniProt V. cholerae 10/21/2013

UniProt V. cholerae 10/21/2013

Dondi Week 9

2013-10-31T17:13:00Z

Dondi: /* Export Information */ Link to uploaded OBO XML.

==Export Information==

Version of GenMAPP Builder: 2.0b71

Computer on which export was run: Virtual machine on my laptop

Postgres Database name: vc_dondi_20131022_gmb2b70
* 2.0b70 was used to import; 2.0b71 was used to export and tally (changes from b70 to b71 had to do with export and tally only)

UniProt XML filename: Vc_Dondi_20131021.xml
* UniProt XML version: http://www.uniprot.org/news/2013/10/16/release
* Time taken to import: 3.5 minutes

GO OBO-XML filename: [[Media:Go_daily-termdb-20131021-125457pm.zip | go_daily-termdb-20131021-125457pm.obo-xml ''.zip'' file]]
* GO OBO-XML version: 2013-10-21 12:54:57pm
* Time taken to import:
* Time taken to process:

GOA filename: 46.V_cholerae_ATCC_39315_Dondi-20131021.goa
* ''Direct download from wiki due to network connectivity problems.''
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]):
* Time taken to import:

Name of .gdb file:
* Time taken to export .gdb:
* Upload your file and link to it here.

Note:

==TallyEngine==

Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the PostgreSQL databases (or you can upload and link to a screenshot of the results).

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#XMLPipeDB_Match | Follow the instructions found on this page to run XMLPipeDB match.]]

Are your results the same as you got for the TallyEngine? Why or why not?

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: (for the [[Week 9]] Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download here].

Copy the OriginalRowCounts table and paste it here:

Note:

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

==.gdb Use in GenMAPP==

Note:

===Putting a gene on the MAPP using the GeneFinder window===

* Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

===Coloring a MAPP with expression data===

Note:

===Running MAPPFinder===

Note:

== Compare Gene Database to Outside Resource==

The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.

Note:

Dondi Week 9

2013-10-31T17:10:58Z

Dondi: /* Export Information */ Export information updates; files forthcoming.

==Export Information==

Version of GenMAPP Builder: 2.0b71

Computer on which export was run: Virtual machine on my laptop

Postgres Database name: vc_dondi_20131022_gmb2b70
* 2.0b70 was used to import; 2.0b71 was used to export and tally (changes from b70 to b71 had to do with export and tally only)

UniProt XML filename: Vc_Dondi_20131021.xml
* UniProt XML version: http://www.uniprot.org/news/2013/10/16/release
* Time taken to import: 3.5 minutes

GO OBO-XML filename: go_daily-termdb-20131021-125457pm.obo-xml
* GO OBO-XML version: 2013-10-21 12:54:57pm
* Time taken to import:
* Time taken to process:

GOA filename: 46.V_cholerae_ATCC_39315_Dondi-20131021.goa
* ''Direct download from wiki due to network connectivity problems.''
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]):
* Time taken to import:

Name of .gdb file:
* Time taken to export .gdb:
* Upload your file and link to it here.

Note:

==TallyEngine==

Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the PostgreSQL databases (or you can upload and link to a screenshot of the results).

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#XMLPipeDB_Match | Follow the instructions found on this page to run XMLPipeDB match.]]

Are your results the same as you got for the TallyEngine? Why or why not?

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: (for the [[Week 9]] Assignment, use the "Vc-Std_External_20101022.gdb" as your benchmark, downloadable from [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download here].

Copy the OriginalRowCounts table and paste it here:

Note:

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?

Note:

==.gdb Use in GenMAPP==

Note:

===Putting a gene on the MAPP using the GeneFinder window===

* Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.

Note:

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note:

===Coloring a MAPP with expression data===

Note:

===Running MAPPFinder===

Note:

== Compare Gene Database to Outside Resource==

The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.

Note:

User:Kdahlquist

2013-10-31T16:58:34Z

Dondi: /* Gene Database Source Files */ Add V. cholerae taxon ID and placeholder for GOA.

User:Kdahlquist

2013-10-31T16:54:10Z

Dondi: /* Gene Database Source Files */ Add GO OBO XML to collection.

Main Page

2013-10-31T16:21:10Z

Dondi: /* Course Schedule */ Move presentation day forward.

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Seminars and Events ===

* '''Special Projects Poster Session:''' Thursday, October 31, 12:15-1:30, Seaver First Floor Foyer. To receive extra credit for attending, you must speak with at least five poster presenters and turn in a one page reflection on what you learned by the following Thursday. In your reflection, give the names of the presenters you spoke with and the titles of their posters.
* '''Biology Department Seminar:''' Thursday, November 7, 12:15 PM, SEA 200, Diane Lynch, LMU Biology alumna, Environmental Advisor for ExxonMobil Refining & Supply, ''Careers in Environmental Compliance''
* '''Bioethics Institute Lecture Series:''' Wednesday, November 13, 7:00-8:30 PM, UH1000, Dr. Kevin Fitzgerald, S.J., Georgetown University, ''Regenerative Medicine and the Illusion of Immortality: Promising Future, Perilous Path?''
* '''Biology Department Seminar:''' Tuesday, November 19, 12:15 PM, SEA 200, Dr. Michele Romolini, CURes/US Forest Service postdoc, ''Green Infrastructure for Resilient Cities: Urban Tree Canopy & Environmental Stewardship''

=== Class Locations ===

* October 31: ''lab''
* November 5: ''lab''
* November 7: ''classroom''

== Group Projects ==

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

=== Teams ===

{| style="width: 75%"
| '''[[Chlamydia trachomatis]]'''
| ''[[Streptococcus pneumoniae]]''
| ''[[Leishmania major]]''
| [[Sinorhizobium meliloti]]
|}

=== Guilds ===

{| style="width: 75%"
| [[Project Manager]]
| [[Coder]]
| [[Quality Assurance]]
| [[GenMAPP User]]
|}

=== Undergraduate Library Research Award ===

The projects for this course will qualify for the Hannon Library’s [http://digitalcommons.lmu.edu/ulra/ Undergraduate Library Research Award (ULRA)]. Click on the link if you are interested in this competition.


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 75%"
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:Gleis| Gabriel Leis]]
| [[User:kevinmcgee | Kevin McGee]]
| [[User:Taur.vil|Tauras Vilgalys]]
|-
| [[User:Kgosch | Kurt Gosch]]
| [[User:Slouie | Stephen Louie]]
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Ajvree|Alina Vreeland]]
|-
| [[User:Lena | Lena Hunt]]
| [[User:laurmagee|Lauren Magee]]
| [[User:mpetredi|Mitchell Petredis]]
| [[User:Dwilliams|Dillon Williams]]
|-
| [[User:vkuehn|Viktoria Kuehn]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Ksherbina|Katrina Sherbina]]
|
|}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday morning). In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)
* Basic acquaintance information
* Like a cell/not like a cell; like a computer/not like a computer

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class on MyLMU Connect]

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma
* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]
| style="vertical-align: top" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Moody (2004) Chapter 6 (on MyLMU Connect]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]

[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]

| style="vertical-align: top; background: #eee" |Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides shown in class (MyLMU Connect)]
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

| style="vertical-align: top" | Introduction to relational databases
* Case study from one of the NAR databases: http://www.rhesusbase.org 
* Relating XML structure to relational structure

Test your understanding: http://xkcd.com/327/
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27 and 10/1)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" | Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations part 1
# Hilda - Mitchell
# Kurt - Kevin Meilak
# Tauras - Miles - Lena
# Lauren - Dillon

[[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Database presentations part 2
# Viktoria - Kevin McGee
# Katrina - Gabriel
# Stephen - Alina

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

[https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Campbell & Heyer Chapter 4 (on MyLMU Connect)]

| style="vertical-align: top" | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]

| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" | [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]

Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger et al. (2003) "MAPPFinder"
''Genome Biology'']]
| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Work session to complete DNA Microarray Analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']

[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
| style="vertical-align: top; background: #eee" |
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
* Groups assigned and species chosen
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guest speaker: Librarian Glenn Johnson-Grau
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Annotated bibliography of genomics papers for your species
** Select genome paper for journal club
** Select microarray paper
| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/12)

''Note different due date''

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give four oral presentations in this course. The first three will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The fourth will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.