LMU BioDB 2015 - User contributions [en]

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2017-03-20T16:26:45Z

Kdahlquist: /* Announcements */ commented out old announcements

__NOTOC__
<div style="text-align: center; font-size: 175%">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''BIOL/CMSI 367-01: Biological Databases'''</div>
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Fall 2015</div>

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

== Announcements ==

* To report issues with the configuration of the computers in Seaver 120, please record it on [[Talk:Software_Configuration | this wiki page.]] The complete list of software that should be installed for this course is found [[Software Configuration | here]]. Note that this configuration is Windows-specific. Some software may not be available for a Mac or may look differently.

=== Upcoming Seminars ===

* There are no more seminars for the rest of the semester.



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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User: Malverso | Mary Alverson]]
| style="padding-right: 1em" | [[User:Rlegaspi | Ron Legaspi]]
| style="padding-right: 1em" | [[User:Troque | Trixie Roque]]
| style="padding-right: 1em" | [[User:Jwoodlee | Jake Woodlee]]
|-
| style="padding-right: 1em" | [[User:Nanguiano | Nicole Anguiano]]
| style="padding-right: 1em" | [[User:Blitvak | Brandon Litvak]]
| style="padding-right: 1em" | [[user:Msaeedi23 | Mahrad Saeedi]]
| style="padding-right: 1em" | [[User:Kwyllie | Kevin Wyllie]]
|-
| style="padding-right: 1em" | [[User:Bklein7 | Brandon Klein]]
| style="padding-right: 1em" | [[User:Lenaolufson | Elena Olufson]]
| style="padding-right: 1em" | [[User:Emilysimso | Emily Simso]]
| style="padding-right: 1em" | [[User:Eyanosch | Erich Yanoschik]]
|-
| style="padding-right: 1em" | [[User:Jkuroda | Josh Kuroda]]
| style="padding-right: 1em" | [[User:Vpachec3 | Veronica Pacheco]]
| style="padding-right: 1em" | [[User:Anuvarsh | Anindita Varshneya]]
| style="padding-right: 1em" | [[User:Kzebrows | Kristin Zebrowski]]
|}

{{ Gene Database Project Links }}

== 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 Tuesdays at midnight (Monday night/Tuesday 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 office hours ({{ Dondi Office Hours }}) can be viewed as unofficial lab sessions: use them for IT help or desktop support

=== Part 1: Building Blocks (Genetic Code and Manipulating Text) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>9/1/2015
|
| 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

| rowspan="2" | [[Week 1]]

(due at midnight 9/8)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>9/3/2015
|
[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/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/8/2015
| [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)]

| DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&content_id=_1103141_1 Slides shown in class on MyLMU Connect]
| rowspan="2" | [[Week 2]]

(due at midnight 9/15)

[[Class Journal Week 2]]
|-
!
| Thursday<br/>9/10/2015
| On [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset MyLMUConnect]:

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

Kaji & Kaji (2004) ''Setting the Record Straight''

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

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

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]
| 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.
* Slides shown in class
* [[Media:BIOL367_Fall2015_GeneticCode-GeneExpression.pdf | Genetic Code-Gene Expression Pencil Exercise]]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/15/2015
| [http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford (2015) ''What is Code?'']
* Emphasis on first two sections (“The Man in the Taupe Blazer” and “Let’s Begin”), but feel free to read further

[http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| An overview of computers, networks, files, and databases
* Useful help resource: http://explainshell.com
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| rowspan="2" | [[Week 3]]

(due at midnight 9/22)

[[Class Journal Week 3]]
|-
!
| Thursday<br/>9/17/2015
|
| Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/22/2015
| [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset 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/43/D1/D1.full Introduction to ''NAR'' Database Issue]

[http://scienceblogs.com/digitalbio/2015/01/30/bio-databases-2015/ Commentary on ''NAR'' Database Issue]

| Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/bbcswebdav/pid-1146580-dt-content-rid-1944592_1/courses/M_46692.201530/20150922_HGP_IntroBiolDB.pdf 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]
| rowspan="2" | [[Week 4]]

(due at midnight 9/29)

[[Class Journal Week 4]]
|-
!
| Thursday<br/>9/24/2015
| [[More Text Processing Features]]

[[How to Read XML Files]]
| Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion


{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/29/2015
| [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]

| 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/
| rowspan="2" | [[Week 5]]

(due at midnight 10/6)

[[Class Journal Week 5]]
|-
!
| Thursday<br/>10/1/2015
| 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).
| SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]

{{Course Schedule Divider}}
|-
! style="background-color: #ddf" | 6
| style="background-color: #eef; border: none" | Tuesday<br/>10/6/2015
| style="background-color: #eef; border: none" |
| style="background-color: #eef; border: none" | President Synder’s Inauguration Day
| rowspan="2" | [[Week 6]]

(due at midnight 10/13)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/8/2015
|
| Database presentations
# Nicole, Erich, Kristen, Josh
# Mary, Emily, Brandon L., Kevin
# Lena, Jake, Anu, Veronica
# Ron, Mahrad, Brandon K., Trixie

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]

|}

=== Part 2: Going Deeper (Gene Expression Data and Relational Databases) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/13/2015
| [http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]

[http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

Campbell & Heyer Chapter 4 (on [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1 MyLMU Connect])

DeRisi et al. (1997) [http://www.sciencemag.org/content/278/5338/680.full ''Science'' 278: 680-686.]

| Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&content_id=_1103141_1 Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]
* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]

| rowspan="2" | [[Week 7]]

(due at midnight 10/20)

[[Class Journal Week 7]]
|-
!
| Thursday<br/>10/15/2015
| [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| [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/]

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/20/2015
| [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[http://www.genomebiology.com/content/4/1/R7 Doniger et al. (2003) "MAPPFinder" ''Genome Biology'']
| [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| rowspan="2" | [[Week 8]]

(due at midnight 10/27)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/22/2015
|
| 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]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/27/2015
|
|
* Introduction to XMLPipeDB: export a Gene Database for ''Vibrio cholerae''
** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests due midnight Saturday, October 31
| rowspan="2" | [[Week 9]]

(due at midnight 11/3)

[[Class Journal Week 9]]
|-
!
| Thursday<br/>10/29/2015
| [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'']
|
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Using Microsoft Excel to Compare ID Lists]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
|}

=== Part 3: Integrating for Research (Gene Database Project) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 10
| Tuesday<br/>11/3/2015
|
|
* Annotated bibliography of genomics papers for your species
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
** Select genome paper for journal club
** Select microarray paper
| rowspan="2" | [[Week 10]]

(due at midnight 11/10)


|-
!
| Thursday<br/>11/5/2015
|
| Begin [[Gene_Database_Project | group projects]]

{{Course Schedule Divider}}
|-
! 11
| Tuesday<br/>11/10/2015
|
| Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| rowspan="2" | [[Week 11]]

(due at midnight 11/17)
|-
!
| Thursday<br/>11/12/2015
|
|

* Status report
* Work session

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/17/2015
|
| First Set of Journal Club Presentations
# Emily Simso/Ron Legaspi (Heavy Metal HaterZ)
# Anu Varshneya/Brandon Litvak (GÉNialOMICS)
# Lena Olufson/Mahrad Saeedi (Class Whoppers)
# Kristin Zebrowski and Erich Yanoschik (Oregon Trail Survivors)

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| rowspan="2" | [[Week 12]]

(due at midnight 11/24)

|-
!
| Thursday<br/>11/19/2015
|
|
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/24/2015
|
| Second Set of Journal Club Presentations
# Kevin Wyllie and Veronica Pacheco
# Brandon Klein (Class Whoopers)
# Mary Alverson and Josh Kuroda
# Jake Woodlee/Trixie Roque (Oregon Trail Survivors)

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| '''''No Week 13 assignment'''''

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/26/2015
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>12/1/2015
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at midnight 12/8)
|-
!
| Thursday<br/>12/3/2015
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/8/2015
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at midnight 12/15)
|-
!
| Thursday<br/>12/10/2015
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/15/2015
| style="background: #fee; border: none" |
| style="background: #fee; border: none" | '''Final project presentations 2:00-4:00 PM'''
| style="background: #fee; border: none" |
|-
!
| Friday<br/>12/18/2015 4:30 PM
|
| '''Project deliverables due 4:30 PM'''
|
|}

== 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:''' Life Sciences Building 289
: '''Office Hours:''' Tuesdays 9:00-11:00 AM, Wednesdays 1:30-3:30 PM and by appointment. I keep a sign-up sheet on my office door to facilitate appointment-making.

==== [[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:''' {{Dondi Office Hours}}

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in the Seaver College of Science and Engineering. 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 2:40–3:55pm, Seaver 120 

This is a hands-on, participatory course, thus attendance at all class meetings is required. Each student is allowed two “sick” days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 5% deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. 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 September 4. The withdrawal or credit/no-credit status deadline is November 6.

=== 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 ===

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

# As an LMU Lion, by the [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Lion%27s%20Code.pdf 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.
# You are responsible for your own learning and for being a good class citizen.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
# 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 away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises; however, if they are being used for other purposes and become distracting to you or others, you will be asked to put them away.
# All students are governed by [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Loyola-Marymount-University-Community-Standards-2015-2016.pdf LMU Community Standards Publication]. 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.

=== Course Website ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2015/. You will need to [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php?title=Special:UserLogin&returnto=Main+Page&type=signup 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 [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset BIOL/CMSI 367-01 on MyLMUConnect]. The two cross-listed sections are using the same site, which is listed as "Biological Databases Fall 2015" with no department or course number. The MyLMUConnect site will be used for materials that cannot be made public on this wiki, including grades.

=== E-mail Communication ===

At times we will communicate with the entire class using campus e-mail systems, so it is essential that you regularly check your lion.lmu.edu e-mail address or forward your lion account e-mail to your preferred e-mail address. Messages sent to the instructors at night or on the weekend will be answered the next school day. Please CC both instructors on all e-mail messages related to this class.

=== 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 this wiki or the 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
* [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Special:UserLogin/signup Account for this wiki]
* [https://secure.cs.lmu.edu/ Computer Science account]
* [http://www.github.com GitHub 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-to-day 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

==== University Core Curriculum ====

This course fulfills the following requirements in the University Core Curriculum:
* Integrations: Interdisciplinary Connections
* Upper Division Information Literacy Flag
* Upper Division Oral Communication Flag

=== 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 five 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, individual (10 points each)
| style="text-align: right" | 140
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (3 points each)
| style="text-align: right" | 42
| points
|-
| Oral presentations
| style="text-align: right" | 105
| points 
|-
| Information literacy (additional points added to two journal assignments)
| style="text-align: right" | 24
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''486'''
| '''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 Tuesday PST (''Monday night/Tuesday morning''); consult the schedule for specific due dates for each assignment.
* Each weekly assignment has an individual component and a shared component. You will earn 10 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry. '''''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 on your user talk pages.
* 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:
** Your electronic laboratory notebook and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning
* For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).

==== 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 and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.'''''

==== Final Group Project ====

{{ Gene Database Project Links }}

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, specifically [https://peerj.com/computer-science/ PeerJ Computer Science]. Specific instructions are posted [[Gene Database Project Deliverables|here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 18 at 4:30 PM. The Final Written Report must be completed to receive a passing grade in the course.'''''

==== Extra Credit ====

Students may accumulate up to 12.5 points toward 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 2.5 points with up to 5 seminars (12.5 points) 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 '''''hard copy''''' of your summary of the seminar '''''in class, within one week''''' of the date of the seminar or they will not count as extra credit.

=== 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.

=== 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.” Attempting to gain extra credit for a seminar that you did not attend or assisting another student to do this are examples of academic dishonesty and will be considered a violation of the Honor Code. [http://bulletin.lmu.edu/content.php?catoid=6&navoid=250#LMU_Honor_Code_and_Process 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:BIOL367_Fall2015_HonorCodeAgreement.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/content.php?catoid=6&navoid=250#LMU_Honor_Code_and_Process LMU Honor Code and Process].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [[Media:Avoiding_plagiarism.pptx | Academic Resource Center presentation on plagiarism]] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Americans with Disabilities Act—Special Accommodations ===

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/fall2015/.

Week 1

2016-08-30T05:13:52Z

Kdahlquist: /* Reflection Questions */ moved header down a level

'''This journal entry is due on Tuesday, September 8, at midnight PDT.''' ''(Monday night/Tuesday morning)''

== Overview ==

The purpose of this assignment is three-fold:
# To set up your individual user page on this wiki as an online resume or curriculum vitae (CV). This will allow the instructors and other students in the course to get to know you. This page is also available to the public and can be used as a professional resume/CV.
# To learn the skills needed to edit this wiki and set up your template, which you will use for all subsequent assignments in this course.
# To begin the process of self-reflection on the shared journal page.

== Individual Journal Assignment ==

=== Homework Partners ===

For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). Homework partners for this week are:

* Mary Alverson, Brandon Litvak
* Nicole Anguiano, Ron Legaspi
* Brandon Klein, Mahrad Saeedi
* Josh Kuroda, Elena Olufson
* Trixie Roque, Veronica Pacheco
* Emily Simso, Jake Woodlee
* Anindita Varshneya, Erich Yanoschik
* Kevin Wyllie, Kristen Zebrowski

=== User Page ===

Set up your individual user page on this wiki (accessible via your username at the top of the page). Your user page should take the form of a résumé or, in academic circles, a ''curriculum vitae''. Dr. Dahlquist and Dr. Dionisio have such pages, both within this wiki (user page) and online in general. You may use those as starting points. As students, your information may be different from ours. At a minimum, you should include:

# Name
# Contact Information
#* Email address ''(We recommend that you use do not use a "mailto" link for this, but give your address as username at domain so that web crawlers cannot pick it up and subject your account to spam.)''
#* LMU snail mail address
# Education
#* Major
#* Expected graduation year
#* Upper division courses in biology, chemistry, math, and computer science that you have taken (including those in which you are enrolled this semester)
# Career interests and goals (if you know)
#* Description of any independent research projects in which you have been involved, including:
#** Title of project
#** Mentor's name
#** List of presentations and/or publications resulting from the project
# Work experience
#* Position/title
#* Employer
#* Dates
#* Responsibilities
# Personal interests/hobbies
# What is your favorite aspect of biology and why?
# What is your favorite aspect of computer science and why?
# Feel free to customize your page in any way you wish, bearing in mind that this site is public and that you should present a professional face to the world.

=== Talk Page ===

For quid pro quo, do this as well:
* Write one question that you would like to know about each of us (Drs. [[User_Talk:Kdahlquist|Dahlquist]] and [[User_Talk:Dondi|Dionisio]]) in our respective user talk pages (linked previously), and we will answer them there. Make sure to sign your question with the standard MediaWiki "[http://en.wikipedia.org/wiki/Wikipedia:Signatures signature shortcut]" (four tildes).

=== Individual Concerns (by email) ===

To keep your answers to the following questions private, please send an e-mail to us with answering to the following questions. Note, if your answer to a question is ''no'', you still need to email us with your ''no'' answer:
# Do you have any worries or concerns about this class at this point?
# Is there anything else you would like us to know?

=== Practice your Wiki Skills ===

The previous sections listed the content that you need to provide on the wiki. In formatting your user page, demonstrate '''all''' of the following skills. Find a way to integrate them naturally into the content (e.g., do not say “Here is an image.” and put just any image on the page).

# Every time you edit a page (whether it is a content page or discussion page), '''enter a meaningful description of your change in the ''Summary'' field''' at the bottom of the editor. This allows other users to easily see (say via the [[Special:RecentChanges]] or history pages) what has happened to the page since they last visited it.
# Create a new Wiki page: '''<nowiki>[[new page title]]</nowiki>''' — When you include a non-existent link in a page (say, your user page), the software can tell that this page doesn't exist and colors it red instead of blue/purple. When you click on the red link, you are then given the option to edit (and thus create) the page.
#* We suggest you practice this by creating your Week 2 journal entry page. The name for the page should be in the format "''username'' Week 2" (i.e., that is the text you put between the square brackets when you link to this page).
# Link to a page within our Wiki: '''<nowiki>[[page title|optional visible label]]</nowiki>'''
#* Go to the [[Main_Page#Students | Students]] section of the course home page and link your name to your own user page.
# Link to an external Web page: '''<nowiki>http://address</nowiki>''' or '''<nowiki>[http://address visible label]</nowiki>'''
#* The second form of the link is preferred because it looks neater on the page.

# Use headings: '''<nowiki>=== title ===</nowiki>''' (number of equals signs indicates heading level)
#* By convention, start your largest heading with two equals signs. The single equals sign is for the title of the page and is automatically created when you create the page.
#* Show at least three levels of headers on your page.
# Create a bulleted list: '''*'''
#* Note that you can create sub-bullets underneath by using multiple asterisks, e.g., '''**''', '''***''', etc.
# Create a numbered list: '''#'''
## Note that you can create numbered sub-lists by using multiple number signs, e.g., '''##''', '''###''', etc.
## You can also mix bullets and numbers, e.g., '''*#''', '''#*''', or even '''#*#''', etc.
## Do not skip lines between items in your bulleted or numbered lists, or the wiki will not interpret your syntax correctly.
# "Comment out" your Wiki code: '''<nowiki></nowiki>''' When you "comment out" your wiki code, the code will be visible on the Edit page, but will not be visible on the wiki page itself. "Commenting" is a common practice in coding that is used to explain the meaning of the code for someone else reading it. In this situation, commenting can be used to keep a rough draft of a wiki page invisible until you are ready for it to be seen.
# Upload an image file: ''Click [[Special:Upload|Upload file]] then follow the instructions.''
#* Use the image on your page: '''<nowiki>[[Image:exact-name-of-image-file]]</nowiki>'''
#* '''REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION!''' We suggest you include an image of yourself that would be suitable for a professional resume.
# Upload another type of file (such as .pdf): ''Click [[Special:Upload|Upload file]] then follow the instructions.''
#* Link to the file you uploaded on your Wiki page: '''<nowiki>[[Media:exact-name-of-uploaded-file|visible label]]</nowiki>'''
#* '''REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION!''' We suggest that you include something professional, such as the Word or PDF version of your paper resume, a scientific paper you have written, etc.
# Assign one or more categories to your page: '''<nowiki>[[Category:category name]]</nowiki>''' This creates an automatic "table of contents" for the wiki. When you click on a category link at the bottom of a page, a new page opens giving you a list of all wiki pages that have been assigned that category.
#* Throughout the course, you will use the category '''<nowiki>[[Category:Journal Entry]]</nowiki>''' for all of your individual journal entry pages you create. You will use the category '''<nowiki>[[Category:Shared]]</nowiki>''' for all of the shared journal entry pages you create.
# Use the discussion/talk page to make a comment. Wiki etiquette requires that you sign your comments with your "signature": <nowiki>~~~~</nowiki> '''(4 tildes in a row)'''. These tildes get converted automatically, for example, into: '' [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:43, 13 August 2015 (PDT) ''
#* You can fulfill this by posting your comment on [[User_Talk:KDahlquist|Dr. Dahlquist's]] and [[User_talk:Dondi | Dr. Dionisio's]] user talk pages.
# Create a template for yourself and use it on your user page. A template is a block of wiki text that you want to use over and over again on various pages. Instead of having to either re-type that content or even copy-and-paste it multiple times, you can simply put the content on a special Template page. You then use code to invoke the template on any other page in which you want that text to appear. There are two steps to creating a Template.
#* Create your template page like you would create any other new wiki page, but using the prefix ''Template:'' as part of the page name. For example, your template should be called '''<nowiki>[[Template:username]]</nowiki>'''.
#* Click on the link and put content on this page that you will want to use over and over again. At the minimum, you should use it to create a set of navigation links that you will use in each week's journal entry. Each week as part of your journal assignment, you will be asked to create a link to your user page, the assignment page, your individual journal entry page, and the shared journal page, as well as adding the category "Journal Entry" to your page. If you put these links on your template and then invoke the template on your journal page, this will automatically be taken care of for you. You may also wish to include any other links that you would find useful.
#* Once you have added and saved the content to your Template page, you need to '''''use''''' your template on your user page. To do so, invoke the template by using the following syntax: '''<nowiki>{{Template:username}}</nowiki>''' in the place you wish the content of the template page to appear. This will "expand" the template to its full contents on the actual page.

== Shared Journal Assignment ==

* Store your journal entry in the shared [[Class Journal Week 1]] page. If this page does not exist yet, go ahead and create it (congratulations on getting in first ''':)''' )
* Link to your journal entry from your user page.
* Link back from the journal entry to your user page.
**'''''NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.'''''
* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

=== Read and Reflect ===

* Answer the "before" set of reflection questions at the end of this assignment.
* Read the two papers by Peter Denning that were given out in class. Read [http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] first, then [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''].
* Read [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr.
* Answer the "after" set of reflection questions at the end of this assignment.

==== Reflection Questions ====

''Before'' reading the Denning articles (on your honor), answer the following questions;
# When you hear the term ''computer science'', what comes to mind?
# When older relatives or friends hear the term ''computer science'', what do you think comes to ''their'' minds?
# When younger relatives or friends hear the term ''computer science'', what do you think comes to their minds?

''Before'' reading the Janovy chapter (on your honor), answer the following questions;
# When you hear the term ''biology'', what comes to mind?
# Do you consider yourself a ''biologist''? why or why not?

''After'' reading the Denning articles and the Janovy chapter, answer the following questions:
# What was the purpose of these readings?
# Which of the voices in the ''Voices of Computing'' article seem to appeal to you the most?
# Apply one of the seven principles from the ''Computing is a Natural Science'' article to something as "non-computer-science"-y as possible, either from other subjects or your daily life.
# What did you find most interesting or provocative about the Janovy reading?
# What does it mean to ''be'' a biologist? Do you consider yourself a biologist? Why or why not?

[[Category:Assignment]]

Gene Database Project Deliverables

2016-01-22T20:20:52Z

Kdahlquist: /* Group Files and Datasets */ comment to ask for ReadMe as .doc and link to Gene Database Testing Report

{{Gene Database Project Links}}

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

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

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== 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:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
</gallery>

* 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 from your [[Week 11|journal club outline and presentation]].
* 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.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.
# 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 a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
* Gene Database Schema figure
* Gene Database Testing Report on final version of Gene Database (can be put at the end of the report as an Appendix)
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
*** Write a paragraph interpreting the GO results in light of the experiment performed in the published paper.
** 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.
** In particular, compare directly the log fold change value of a couple of key genes mentioned in the paper with what you found for those genes.
** Compare the criteria the journal article used for a significant expression change to the criteria that you used. How many genes met the criterion for the article vs. how many met the criterion for your analysis.

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings.
* How closely do your findings correspond to the original study?
* Are there significant differences?
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 18 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
# Background on your species and your species' genome from the genome paper presentation.
# The results of the Gene Database creation
#* Gene Database Schema figure
#* A table that summarizes how many OrderedLocusNames IDs were found
#** by XMLPipeDB match in the UniProt XML file
#** by TallyEngine in the UniProt XML file
#** by TallyEngine in the PostgreSQL database
#** in the OriginalRowCounts table in the gdb
#** in your external model organism database source
#* Give the command used in match to generate these results
#* Give the query used in PGAdmin III to generate these results
#* Include a screenshot of the TallyEngine results as a figure
#* Report on quantity and identity of gene IDs that did not make it into the database
#*# OrderedLocusNames IDs that were not in the XML source at all
#*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
#*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
#* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
# Introduce the experiment performed in the microarray paper, including the experimental design flow chart
# Report results of the DNA microarray analysis
#* Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
#* Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
#* Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
#** Show a list of 15-20 non-redundant GO terms.
#** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
#* GenMAPP MAPP of a pathway relevant to your results
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, December 15.'''''
** 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 evaluated by the instructors using the [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Group Files and Datasets ==

* 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]]
** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:GenMAPP_schema_generic_bacteria_20151210.zip | GenMAPP_schema_generic_bacteria_20151210.zip]] 
*** Sample schema in jpeg format: [[Media:GenMAPP_schema_generic_bacteria_20151210.jpg | GenMAPP_schema_generic_bacteria_20151210.jpg]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file) 
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

== 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 or as a Word document uploaded to your group deliveables 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?

{{Gene Database Project Links}}

[[Category:Group Projects]]

Week 2

2016-01-06T20:55:27Z

Kdahlquist: Undo revision 6137 by Bklein7 (talk)assignment page was wrongly copied over to make team page

'''This journal entry is due on Tuesday, September 15, at midnight PDT.''' ''(Monday night/Tuesday morning)''



== Overview ==

The purpose of this assignment is:

* To familiarize yourself with the decoding the genetic code in a "paper and pencil" exercise, to motivate using a computer to do such work.
* To begin comparing the genetic code to a computer code.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 2" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual wiki page. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

=== Homework Partners ===

For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). Homework partners for this week are:

* Mary Alverson, Elena Olufson
* Nicole Anguiano, Brandon Litvak
* Brandon Klein, Emily Simso
* Josh Kuroda, Veronica Pacheco
* Ron Legaspi, Trixie Roque
* Mahrad Saeedi, Anindita Varshneya
* Jake Woodlee, Kevin Wyllie
* Erich Yanoschik, Kristen Zebrowski



=== The Genetic Code ===

* Write out the complementary strand of DNA below the strand shown and be sure to label the 5’ and 3’ ends of the complementary strand.

5’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’

* There are six possible reading frames in double-stranded DNA. Using the [http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table genetic code], translate all possible reading frames of this DNA sequence, keeping in mind the following rules.
** In RNA, the T becomes a U, so everywhere you see a T in the sequence, read it as a U.
** The genetic code is read in the 5’ to 3’ direction.
** Use the single-letter abbreviations for the amino acids because that is what is commonly used by computer programs.
* Wiki Hint: if you start your line with a single space character, it will appear in the grey box surrounded by the dashed line as shown above.
* Which of the reading frames (if any) of the reading frames you translated is an ''open reading frame'', i.e., does not contain a stop codon?
** By convention, the top strand frames are called +1, +2, +3, reading 5' to 3' and the bottom strand frames are called -1, -2, -3, reading 5' to 3'.

== Shared Journal Assignment ==

* Store your journal entry in the shared [[Class Journal Week 2]] page. If this page does not exist yet, go ahead and create it (congratulations on getting in first ''':)''' )
* Link to your journal entry from your user page.
* Link back from the journal entry to your user page.
**'''''NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.'''''
* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

=== Read ===

* [http://www.ncbi.nlm.nih.gov/books/NBK21121/#A5818 Brown, T.A. (2002) ''Genomes 2'', Ch. 3.3.2: The link between the transcriptome and the proteome] (freely available on NCBI Bookshelf)
* Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account. ''Trends in Biochemical Sciences'' 29: 46-54. (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])
* Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight. ''Trends in Biochemical Sciences'' 29: 293.
* Moody, G. (2004) ''Digital Code of Life'', Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (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])
* Hayes, B. (2004) Ode to the Code, ''American Scientist'' 92: 494-498. (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])

=== Reflect ===

# What is the biggest discovery that I made from these readings?
# What part of the readings did I understand the least?
# What is the relationship between the genetic code and a computer code?

[[Category:Assignment]]

Week 2

2016-01-06T20:54:36Z

Kdahlquist: Undo revision 6146 by Bklein7 (talk)systematically undoing mistaken edits

= Team Information & Links =

{{Template:Class Whoopers}}

=Weekly Updates=
==Week 11==
===Goals===
* For all:
** Outline your assigned paper on your user page and include a list of 10 defined terms from the paper.
*Nicole & Brandon
**Prepare Journal Club presentation on the designated genome sequencing article
**Slides Due: by midnight, Tuesday, November 17
**Presentation Date: Tuesday, November 24
*Lena & Mahrad
**Prepare Journal Club presentation on the designated microarray paper
**Slides Due: by midnight, Tuesday, November 17
**Presentation Date: Tuesday, November 17

===Progress===
*Nicole Anguiano (Coder):
*Brandon Klein (QA):
*Lena Olufson (GennMAPP):
*Mahrad Saeedi (GennMAPP):

=== Meetings! ===
* TBD

==Week 10==
===Goals===
* For all:
** Create an annotated bibliography including one genome sequencing paper and two microarray experiments for Bordetella pertussis
** Create/update team page & compile group annotated bibliography
** Assignment due date: Midnight Tuesday, November 10

===Progress===
*All group members created annotated bibliographies and compiled them on the newly created group page.

=== Meetings! ===
* Monday, November 9, 8pm-9pm, Seaver 120

= Deliverables =
*GenMAPP Gene Database for assigned species (.gdb)
*ReadMe file to accompany the Gene Database (.pdf)
*Sample ReadMe in Word format: ReadMe_Vc-Std_External_20131122.zip
*Include Gene Database Schema diagram in ReadMe
*Sample schema in Adobe Illustrator format: 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)
*Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf)
*PowerPoint presentation (.ppt, given on Tuesday, December 15)

= Annotated Bibliography =
== Genome Sequencing Paper ==

Neither of these papers is the ''first'' to report the genome sequence of ''B. pertussis.'' The paper that you will want to use is [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html this one]. I found it by looking at the introduction and references of the Zhang et. al (2011) paper. For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003). You will use the Parkhill paper for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:54, 10 November 2015 (PST)''

Note: revise/complete this citation

*Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., et al. (2003). Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nature genetics, 35(1), 32-40. doi:10.1038/ng1227
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/12910271
* PubMed Central: Not available on PubMed Central
* Publisher Full Text (HTML): http://www.nature.com/ng/journal/v35/n1/full/ng1227.html
* Publisher Full Text (PDF): http://www.nature.com/ng/journal/v35/n1/pdf/ng1227.pdf
* Copyright: ©2003 Nature Publishing Group (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication
* Publisher: Nature Publishing Group (for profit?)
* Availability: in print and online
* Did LMU pay a fee for this article: Yes, LMU pays a subscription fee for access to the journal ''Nature Genetics''.

== Microarray Paper ==

This paper is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:04, 10 November 2015 (PST)''

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE, 9(12):e115243. doi: 10.1371/journal.pone.0115243
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25501560
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264864/
* Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243
* Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0115243&representation=PDF
* Copyright: © 2014 Hoo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. (info found [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243 here])
* Publisher: PLOS ONE (respected open access organization)
* Availability: online only
* Did LMU pay a fee for this article: no
* Web site where the data resides: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62088 NCBI GEO data]

Week 2

2016-01-06T20:53:46Z

Kdahlquist: Undo revision 6147 by Bklein7 (talk)wrong page was redirected

Week 11

2015-12-17T23:11:58Z

Kdahlquist: /* Journal Club Presentation */ changed emphasis on linking from individual and team pages

'''This journal entry is due on Tuesday, November 17, at midnight PST.''' ''(Monday night/Tuesday morning)''

* The Individual Journal Assignment (vocabulary and outline) is worth a total of 10 points (as usual).
* The journal club presentation is worth a total of 35 points (each member of a pair will receive the same grade).
* The Team Journal Assignment is worth a total of 3 points (as usual).

== Overview ==

For this week, your team has two main tasks:

# Prepare for journal club presentations in Weeks 12 and 13
#* You will deeply explore and perform a critical review of the genome paper (coder/QA) and microarray paper (GenMAPP users) for your team's species.
#* You will communicate your findings in an effective oral presentation.
# Begin initial tasks on your research project
#* Coder/QA
#** Set up coding/testing environment
#** Determine the regular expression for the ordered locus ID for your species
#** Identify the appropriate model organism database for your species.
#** Perform an initial Gene Database export and Gene Database Testing Report
#* GenMAPP Users
#** Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
#** Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
#** Compile the raw data in preparation for normalization and statistical analysis.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Link from your journal entry to your team's home page.
* Link from your team's home page to your journal entry.
* Don't forget to add the categories "Journal Entry", "Group Projects", and your team's category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template (and your team's template) and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

=== Preparation for Journal Club on Your Species ===

Your team will split into two halves for journal club presentations that will take place in class on Tuesday, November 17 and Tuesday, November 24. The Coder and Quality Assurance person will present the genome paper for your species and the GenMAPP Users will present the microarray paper for your species. You will decide within your team who will present on which day. Please edit the schedule on the [[Main Page]] to show who is presenting on which day.

In preparation for your journal club presentation, 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).
#* For the genome paper (Coder and QA only): in addition to the journal article, please find and review the Model Organism Database (MOD) for your species similarly to what you did to review your assigned database for the ''NAR'' assignment. 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 (the "ordered locus name" ID)? (for example, for ''Vibrio cholerae'' it was VC#### or VC_####).
#* For the microarray paper (GenMAPP Users only), include the following:
#*# Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
#*# Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
#*# Construct a flow chart that illustrates the above.

=== Journal Club Presentation ===

Each pair of students will prepare and give a 15 minute PowerPoint presentation for their paper in class on Tuesday, November 17 or Tuesday, November 24.
* 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 17, '''even if you are presenting the following week.'''''
** 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 [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? 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 ==

* Please make the requested changes to your team's wiki pages.
** Please "comment out" the microarray papers that you won't be using for the project, just leaving the annotated bibliographic information for your genome paper and the microarray paper you will be using.
* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
* Set up a system for managing team files, including a filename system that keeps track of versions of files.



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

Week 12

2015-12-17T22:36:33Z

Kdahlquist: /* Team Journal Assignment */ next time add reflection questions

'''This journal entry is due on Tuesday, November 24, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The purpose of this assignment is to set team goals and make progress on your team projects.

== Individual Journal Assignment ==

* 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).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).



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

Week 11

2015-12-17T22:35:42Z

Kdahlquist: /* Team Journal Assignment */ note for reflection questions next year

'''This journal entry is due on Tuesday, November 17, at midnight PST.''' ''(Monday night/Tuesday morning)''

* The Individual Journal Assignment (vocabulary and outline) is worth a total of 10 points (as usual).
* The journal club presentation is worth a total of 35 points (each member of a pair will receive the same grade).
* The Team Journal Assignment is worth a total of 3 points (as usual).

== Overview ==

For this week, your team has two main tasks:

# Prepare for journal club presentations in Weeks 12 and 13
#* You will deeply explore and perform a critical review of the genome paper (coder/QA) and microarray paper (GenMAPP users) for your team's species.
#* You will communicate your findings in an effective oral presentation.
# Begin initial tasks on your research project
#* Coder/QA
#** Set up coding/testing environment
#** Determine the regular expression for the ordered locus ID for your species
#** Identify the appropriate model organism database for your species.
#** Perform an initial Gene Database export and Gene Database Testing Report
#* GenMAPP Users
#** Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
#** Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
#** Compile the raw data in preparation for normalization and statistical analysis.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Link from your journal entry to your team's home page.
* Link from your team's home page to your journal entry.
* Don't forget to add the categories "Journal Entry", "Group Projects", and your team's category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template (and your team's template) and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

=== Preparation for Journal Club on Your Species ===

Your team will split into two halves for journal club presentations that will take place in class on Tuesday, November 17 and Tuesday, November 24. The Coder and Quality Assurance person will present the genome paper for your species and the GenMAPP Users will present the microarray paper for your species. You will decide within your team who will present on which day. Please edit the schedule on the [[Main Page]] to show who is presenting on which day.

In preparation for your journal club presentation, 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).
#* For the genome paper (Coder and QA only): in addition to the journal article, please find and review the Model Organism Database (MOD) for your species similarly to what you did to review your assigned database for the ''NAR'' assignment. 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 (the "ordered locus name" ID)? (for example, for ''Vibrio cholerae'' it was VC#### or VC_####).
#* For the microarray paper (GenMAPP Users only), include the following:
#*# Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
#*# Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
#*# Construct a flow chart that illustrates the above.

=== Journal Club Presentation ===

Each pair of students will prepare and give a 15 minute PowerPoint presentation for their paper in class on Tuesday, November 17 or Tuesday, November 24.
* 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 17, even if you are presenting the following week.'''''
** 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 [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? 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 ==

* Please make the requested changes to your team's wiki pages.
** Please "comment out" the microarray papers that you won't be using for the project, just leaving the annotated bibliographic information for your genome paper and the microarray paper you will be using.
* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
* Set up a system for managing team files, including a filename system that keeps track of versions of files.



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

Week 10

2015-12-16T22:47:55Z

Kdahlquist: /* Annotated Bibliography of Genomics Papers for your Species */ clarify what link to data means

'''This journal entry is due on Tuesday, November 10, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The two main objectives of this week's exercise is to:
# [[Week_10#Team_Journal_Assignment | Create your team's home page, select your species, and select your Project Manager.]]
# Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
#* Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 15 points (instead of 10).
* Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

'''Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.'''

=== Annotated Bibliography of Genomics Papers for your Species ===

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
*# The journal article which describes the results of the whole genome sequencing for your species. ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)'' 
*#* Use a keyword search for each of these databases/tools and answer the following:
*#** '''PubMed'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Google Scholar'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Web of Science'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Use the advanced search functions for each of these three databases/tools and answer the following:
*#** '''PubMed'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Google Scholar'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Web of Science'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get? 
*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide]) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
*#** The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
*#** The link to the full text of the article (HTML format) from the publisher web site. 
*#** The link to the full PDF version of the article from the publisher web site.
*#** Who owns the rights to the article?
*#*** Does the journal own the copyright?
*#*** Do the authors own the copyright?
*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? 
*#*** Is the article available “Open Access”?
*#** What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
*#** Is this article available in print or online only? 
*#** Has LMU paid a subscription or other fee for your access to this article? 
*#*** A list of the journals LMU pays for access to can be found [http://sq4ya5rf2q.search.serialssolutions.com here].
*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
*#* Give an overview of the results of the search.
*#** How many articles does this article cite?
*#** How many articles cite this article?
*#** Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*# Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
*#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
*#** The control sample needs to be derived from mRNA and not genomic DNA.
*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
*#* We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
*#* State what you used as search terms and what type of search terms they were.
*#* Give an overview of the results of the search.
*#** How many results did you get?
*#** Give an assessment of how relevant the results were.
*#* For each article, please provide all of the same information that you provided for the genome article above. 
*#* In addition, you must also link to the web site where the microarray data resides.
*#** For each of the microarray articles/datasets, answer the following:
*#**# What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
*#**# Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
*#** Remember, microarray data is not centrally located on the web. Some major sources are:
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
*#**** Click on the link to "Browse ArrayExpress"
*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
* Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
* Publisher: American Society for Cell Biology (scientific society)
* Availability: in print and online
* Did LMU pay a fee for this article: no

== Team Journal Assignment ==

=== Team Membership ===

The project groups are:
# '''Heavy Metal HaterZ''' (a.k.a. Team 1 a.k.a the best team) - ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
# '''Class Whoopers''' - ''Bordetella pertussis''
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
# '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya (Project Manager)
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
# '''Oregon Trail Survivors''' - ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristen Zebrowski

* Choose one member of your team to be the Project Manager. Only ''one'' member of the team will serve in this role (no co-Project Managers). Record this information on the [[Gene_Database_Project | Group Project page]] and on your team's home page.

=== Selecting Your Team's Species ===

Each team will choose from among the species shown below:

* ''Burkholderia cenocepacia''
* ''Bordetella pertussis''
* ''Shewanella oneidensis''
* ''Shigella flexneri''

=== Creating a Team Wiki Page ===

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
* Name your team and create your team home page on the wiki.
** The name of your team home page should simply be the team name.
** This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
** Create a link to your team's page on the course Main page.
** Create a category using your team name and use it on your team's main page and all pages you will create for the project. Also use the category "Group Projects" on your team's pages.
** Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
* On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

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

Week 10

2015-12-16T21:50:28Z

Kdahlquist: /* Annotated Bibliography of Genomics Papers for your Species */ clarify that need to do cited reference search for microarray articles as well

'''This journal entry is due on Tuesday, November 10, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The two main objectives of this week's exercise is to:
# [[Week_10#Team_Journal_Assignment | Create your team's home page, select your species, and select your Project Manager.]]
# Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
#* Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 15 points (instead of 10).
* Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

'''Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.'''

=== Annotated Bibliography of Genomics Papers for your Species ===

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
*# The journal article which describes the results of the whole genome sequencing for your species. ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)'' 
*#* Use a keyword search for each of these databases/tools and answer the following:
*#** '''PubMed'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Google Scholar'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Web of Science'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Use the advanced search functions for each of these three databases/tools and answer the following:
*#** '''PubMed'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Google Scholar'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Web of Science'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get? 
*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide]) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
*#** The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
*#** The link to the full text of the article (HTML format) from the publisher web site. 
*#** The link to the full PDF version of the article from the publisher web site.
*#** Who owns the rights to the article?
*#*** Does the journal own the copyright?
*#*** Do the authors own the copyright?
*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? 
*#*** Is the article available “Open Access”?
*#** What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
*#** Is this article available in print or online only? 
*#** Has LMU paid a subscription or other fee for your access to this article? 
*#*** A list of the journals LMU pays for access to can be found [http://sq4ya5rf2q.search.serialssolutions.com here].
*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
*#* Give an overview of the results of the search.
*#** How many articles does this article cite?
*#** How many articles cite this article?
*#** Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*# Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
*#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
*#** The control sample needs to be derived from mRNA and not genomic DNA.
*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
*#* We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
*#* State what you used as search terms and what type of search terms they were.
*#* Give an overview of the results of the search.
*#** How many results did you get?
*#** Give an assessment of how relevant the results were.
*#* For each article, please provide all of the same information that you provided for the genome article above. 
*#* In addition, you must also link to the web site where the microarray data resides.
*#** For each of the microarray articles/datasets, answer the following:
*#**# What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
*#**# Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
*#** Remember, microarray data is not centrally located on the web. Some major sources are:
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
*#**** Click on the link to "Browse ArrayExpress"
*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
* Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
* Publisher: American Society for Cell Biology (scientific society)
* Availability: in print and online
* Did LMU pay a fee for this article: no

== Team Journal Assignment ==

=== Team Membership ===

The project groups are:
# '''Heavy Metal HaterZ''' (a.k.a. Team 1 a.k.a the best team) - ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
# '''Class Whoopers''' - ''Bordetella pertussis''
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
# '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya (Project Manager)
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
# '''Oregon Trail Survivors''' - ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristen Zebrowski

* Choose one member of your team to be the Project Manager. Only ''one'' member of the team will serve in this role (no co-Project Managers). Record this information on the [[Gene_Database_Project | Group Project page]] and on your team's home page.

=== Selecting Your Team's Species ===

Each team will choose from among the species shown below:

* ''Burkholderia cenocepacia''
* ''Bordetella pertussis''
* ''Shewanella oneidensis''
* ''Shigella flexneri''

=== Creating a Team Wiki Page ===

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
* Name your team and create your team home page on the wiki.
** The name of your team home page should simply be the team name.
** This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
** Create a link to your team's page on the course Main page.
** Create a category using your team name and use it on your team's main page and all pages you will create for the project. Also use the category "Group Projects" on your team's pages.
** Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
* On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

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

Week 10

2015-12-16T20:40:19Z

Kdahlquist: /* Annotated Bibliography of Genomics Papers for your Species */ note that need to italicize journal name

'''This journal entry is due on Tuesday, November 10, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The two main objectives of this week's exercise is to:
# [[Week_10#Team_Journal_Assignment | Create your team's home page, select your species, and select your Project Manager.]]
# Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
#* Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 15 points (instead of 10).
* Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

'''Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.'''

=== Annotated Bibliography of Genomics Papers for your Species ===

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
*# The journal article which describes the results of the whole genome sequencing for your species. ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)'' 
*#* Use a keyword search for each of these databases/tools and answer the following:
*#** '''PubMed'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Google Scholar'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Web of Science'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Use the advanced search functions for each of these three databases/tools and answer the following:
*#** '''PubMed'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Google Scholar'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Web of Science'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get? 
*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide]) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
*#** The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
*#** The link to the full text of the article (HTML format) from the publisher web site. 
*#** The link to the full PDF version of the article from the publisher web site.
*#** Who owns the rights to the article?
*#*** Does the journal own the copyright?
*#*** Do the authors own the copyright?
*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? 
*#*** Is the article available “Open Access”?
*#** What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
*#** Is this article available in print or online only? 
*#** Has LMU paid a subscription or other fee for your access to this article? 
*#*** A list of the journals LMU pays for access to can be found [http://sq4ya5rf2q.search.serialssolutions.com here].
*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
*#* Give an overview of the results of the search.
*#** How many articles does this article cite?
*#** How many articles cite this article?
*#** Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*# Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
*#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
*#** The control sample needs to be derived from mRNA and not genomic DNA.
*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
*#* We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
*#* State what you used as search terms and what type of search terms they were.
*#* Give an overview of the results of the search.
*#** How many results did you get?
*#** Give an assessment of how relevant the results were.
*#* For each article, please provide all of the same information that you provided for the genome article above.
*#* In addition, you must also link to the web site where the microarray data resides.
*#** For each of the microarray articles/datasets, answer the following:
*#**# What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
*#**# Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
*#** Remember, microarray data is not centrally located on the web. Some major sources are:
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
*#**** Click on the link to "Browse ArrayExpress"
*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
* Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
* Publisher: American Society for Cell Biology (scientific society)
* Availability: in print and online
* Did LMU pay a fee for this article: no

== Team Journal Assignment ==

=== Team Membership ===

The project groups are:
# '''Heavy Metal HaterZ''' (a.k.a. Team 1 a.k.a the best team) - ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
# '''Class Whoopers''' - ''Bordetella pertussis''
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
# '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya (Project Manager)
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
# '''Oregon Trail Survivors''' - ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristen Zebrowski

* Choose one member of your team to be the Project Manager. Only ''one'' member of the team will serve in this role (no co-Project Managers). Record this information on the [[Gene_Database_Project | Group Project page]] and on your team's home page.

=== Selecting Your Team's Species ===

Each team will choose from among the species shown below:

* ''Burkholderia cenocepacia''
* ''Bordetella pertussis''
* ''Shewanella oneidensis''
* ''Shigella flexneri''

=== Creating a Team Wiki Page ===

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
* Name your team and create your team home page on the wiki.
** The name of your team home page should simply be the team name.
** This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
** Create a link to your team's page on the course Main page.
** Create a category using your team name and use it on your team's main page and all pages you will create for the project. Also use the category "Group Projects" on your team's pages.
** Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
* On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

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

Week 10

2015-12-16T19:51:48Z

Kdahlquist: /* Annotated Bibliography of Genomics Papers for your Species */ note to ask more explicitly about evaluating searches

'''This journal entry is due on Tuesday, November 10, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The two main objectives of this week's exercise is to:
# [[Week_10#Team_Journal_Assignment | Create your team's home page, select your species, and select your Project Manager.]]
# Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
#* Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 15 points (instead of 10).
* Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

'''Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.'''

=== Annotated Bibliography of Genomics Papers for your Species ===

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
*# The journal article which describes the results of the whole genome sequencing for your species. ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)'' 
*#* Use a keyword search for each of these databases/tools and answer the following:
*#** '''PubMed'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Google Scholar'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Web of Science'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Use the advanced search functions for each of these three databases/tools and answer the following:
*#** '''PubMed'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Google Scholar'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Web of Science'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get? 
*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide]) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
*#** The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
*#** The link to the full text of the article (HTML format) from the publisher web site. 
*#** The link to the full PDF version of the article from the publisher web site.
*#** Who owns the rights to the article?
*#*** Does the journal own the copyright?
*#*** Do the authors own the copyright?
*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? 
*#*** Is the article available “Open Access”?
*#** What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
*#** Is this article available in print or online only? 
*#** Has LMU paid a subscription or other fee for your access to this article? 
*#*** A list of the journals LMU pays for access to can be found [http://sq4ya5rf2q.search.serialssolutions.com here].
*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
*#* Give an overview of the results of the search.
*#** How many articles does this article cite?
*#** How many articles cite this article?
*#** Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*# Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
*#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
*#** The control sample needs to be derived from mRNA and not genomic DNA.
*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
*#* We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
*#* State what you used as search terms and what type of search terms they were.
*#* Give an overview of the results of the search.
*#** How many results did you get?
*#** Give an assessment of how relevant the results were.
*#* For each article, please provide all of the same information that you provided for the genome article above.
*#* In addition, you must also link to the web site where the microarray data resides.
*#** For each of the microarray articles/datasets, answer the following:
*#**# What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
*#**# Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
*#** Remember, microarray data is not centrally located on the web. Some major sources are:
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
*#**** Click on the link to "Browse ArrayExpress"
*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
* Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
* Publisher: American Society for Cell Biology (scientific society)
* Availability: in print and online
* Did LMU pay a fee for this article: no

== Team Journal Assignment ==

=== Team Membership ===

The project groups are:
# '''Heavy Metal HaterZ''' (a.k.a. Team 1 a.k.a the best team) - ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
# '''Class Whoopers''' - ''Bordetella pertussis''
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
# '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya (Project Manager)
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
# '''Oregon Trail Survivors''' - ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristen Zebrowski

* Choose one member of your team to be the Project Manager. Only ''one'' member of the team will serve in this role (no co-Project Managers). Record this information on the [[Gene_Database_Project | Group Project page]] and on your team's home page.

=== Selecting Your Team's Species ===

Each team will choose from among the species shown below:

* ''Burkholderia cenocepacia''
* ''Bordetella pertussis''
* ''Shewanella oneidensis''
* ''Shigella flexneri''

=== Creating a Team Wiki Page ===

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
* Name your team and create your team home page on the wiki.
** The name of your team home page should simply be the team name.
** This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
** Create a link to your team's page on the course Main page.
** Create a category using your team name and use it on your team's main page and all pages you will create for the project. Also use the category "Group Projects" on your team's pages.
** Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
* On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

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

Week 10

2015-12-16T19:34:49Z

Kdahlquist: /* Annotated Bibliography of Genomics Papers for your Species */ note about confusion about HTML version and other notes for next time

'''This journal entry is due on Tuesday, November 10, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The two main objectives of this week's exercise is to:
# [[Week_10#Team_Journal_Assignment | Create your team's home page, select your species, and select your Project Manager.]]
# Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
#* Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 15 points (instead of 10).
* Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

'''Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.'''

=== Annotated Bibliography of Genomics Papers for your Species ===

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
*# The journal article which describes the results of the whole genome sequencing for your species. ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)'' 
*#* Use a keyword search for each of these databases/tools and answer the following:
*#** '''PubMed'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Google Scholar'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Web of Science'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Use the advanced search functions for each of these three databases/tools and answer the following:
*#** '''PubMed'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Google Scholar'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Web of Science'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide]) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
*#** The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
*#** The link to the full text of the article (HTML format) from the publisher web site. 
*#** The link to the full PDF version of the article from the publisher web site.
*#** Who owns the rights to the article?
*#*** Does the journal own the copyright?
*#*** Do the authors own the copyright?
*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? 
*#*** Is the article available “Open Access”?
*#** What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
*#** Is this article available in print or online only? 
*#** Has LMU paid a subscription or other fee for your access to this article? 
*#*** A list of the journals LMU pays for access to can be found [http://sq4ya5rf2q.search.serialssolutions.com here].
*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
*#* Give an overview of the results of the search.
*#** How many articles does this article cite?
*#** How many articles cite this article?
*#** Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*# Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
*#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
*#** The control sample needs to be derived from mRNA and not genomic DNA.
*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
*#* We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
*#* State what you used as search terms and what type of search terms they were.
*#* Give an overview of the results of the search.
*#** How many results did you get?
*#** Give an assessment of how relevant the results were.
*#* For each article, please provide all of the same information that you provided for the genome article above.
*#* In addition, you must also link to the web site where the microarray data resides.
*#** For each of the microarray articles/datasets, answer the following:
*#**# What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
*#**# Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
*#** Remember, microarray data is not centrally located on the web. Some major sources are:
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
*#**** Click on the link to "Browse ArrayExpress"
*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
* Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
* Publisher: American Society for Cell Biology (scientific society)
* Availability: in print and online
* Did LMU pay a fee for this article: no

== Team Journal Assignment ==

=== Team Membership ===

The project groups are:
# '''Heavy Metal HaterZ''' (a.k.a. Team 1 a.k.a the best team) - ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
# '''Class Whoopers''' - ''Bordetella pertussis''
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
# '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya (Project Manager)
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
# '''Oregon Trail Survivors''' - ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristen Zebrowski

* Choose one member of your team to be the Project Manager. Only ''one'' member of the team will serve in this role (no co-Project Managers). Record this information on the [[Gene_Database_Project | Group Project page]] and on your team's home page.

=== Selecting Your Team's Species ===

Each team will choose from among the species shown below:

* ''Burkholderia cenocepacia''
* ''Bordetella pertussis''
* ''Shewanella oneidensis''
* ''Shigella flexneri''

=== Creating a Team Wiki Page ===

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
* Name your team and create your team home page on the wiki.
** The name of your team home page should simply be the team name.
** This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
** Create a link to your team's page on the course Main page.
** Create a category using your team name and use it on your team's main page and all pages you will create for the project. Also use the category "Group Projects" on your team's pages.
** Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
* On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

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

Week 10

2015-12-16T19:33:01Z

Kdahlquist: /* Annotated Bibliography of Genomics Papers for your Species */ note for next time about finding main genome paper, not for substrain

'''This journal entry is due on Tuesday, November 10, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The two main objectives of this week's exercise is to:
# [[Week_10#Team_Journal_Assignment | Create your team's home page, select your species, and select your Project Manager.]]
# Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
#* Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 15 points (instead of 10).
* Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

'''Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.'''

=== Annotated Bibliography of Genomics Papers for your Species ===

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
*# The journal article which describes the results of the whole genome sequencing for your species. ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)'' 
*#* Use a keyword search for each of these databases/tools and answer the following:
*#** '''PubMed'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Google Scholar'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#** '''Web of Science'''
*#*** What original keyword(s) did you use? How many results did you get?
*#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
*#* Use the advanced search functions for each of these three databases/tools and answer the following:
*#** '''PubMed'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Google Scholar'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#** '''Web of Science'''
*#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide]) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
*#** The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
*#** The link to the full text of the article (HTML format) from the publisher web site.
*#** The link to the full PDF version of the article from the publisher web site.
*#** Who owns the rights to the article?
*#*** Does the journal own the copyright?
*#*** Do the authors own the copyright?
*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license?
*#*** Is the article available “Open Access”?
*#** What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
*#** Is this article available in print or online only?
*#** Has LMU paid a subscription or other fee for your access to this article?
*#*** A list of the journals LMU pays for access to can be found [http://sq4ya5rf2q.search.serialssolutions.com here].
*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
*#* Give an overview of the results of the search.
*#** How many articles does this article cite?
*#** How many articles cite this article?
*#** Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
*# Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
*#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
*#** The control sample needs to be derived from mRNA and not genomic DNA.
*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
*#* We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
*#* State what you used as search terms and what type of search terms they were.
*#* Give an overview of the results of the search.
*#** How many results did you get?
*#** Give an assessment of how relevant the results were.
*#* For each article, please provide all of the same information that you provided for the genome article above.
*#* In addition, you must also link to the web site where the microarray data resides.
*#** For each of the microarray articles/datasets, answer the following:
*#**# What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
*#**# Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
*#** Remember, microarray data is not centrally located on the web. Some major sources are:
*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
*#**** Click on the link to "Browse ArrayExpress"
*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
* Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
* Publisher: American Society for Cell Biology (scientific society)
* Availability: in print and online
* Did LMU pay a fee for this article: no

== Team Journal Assignment ==

=== Team Membership ===

The project groups are:
# '''Heavy Metal HaterZ''' (a.k.a. Team 1 a.k.a the best team) - ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
# '''Class Whoopers''' - ''Bordetella pertussis''
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
# '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya (Project Manager)
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
# '''Oregon Trail Survivors''' - ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristen Zebrowski

* Choose one member of your team to be the Project Manager. Only ''one'' member of the team will serve in this role (no co-Project Managers). Record this information on the [[Gene_Database_Project | Group Project page]] and on your team's home page.

=== Selecting Your Team's Species ===

Each team will choose from among the species shown below:

* ''Burkholderia cenocepacia''
* ''Bordetella pertussis''
* ''Shewanella oneidensis''
* ''Shigella flexneri''

=== Creating a Team Wiki Page ===

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
* Name your team and create your team home page on the wiki.
** The name of your team home page should simply be the team name.
** This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
** Create a link to your team's page on the course Main page.
** Create a category using your team name and use it on your team's main page and all pages you will create for the project. Also use the category "Group Projects" on your team's pages.
** Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
* On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

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

File:FINAL CompiledRawData RXRP EYKZ20151210.gex

2015-12-12T00:51:00Z

Kdahlquist: Kdahlquist uploaded a new version of File:FINAL CompiledRawData RXRP EYKZ20151210.gex

.gex compiled raw data file for OTS

Gene Database Project

2015-12-10T23:52:12Z

Kdahlquist: /* Group Deliverables */ added generic schema in ai and jpeg formats

{{Gene Database Project Links}}

== Deliverables ==

* You will give a final group [[Gene_Database_Project_Deliverables#PowerPoint_Presentation | PowerPoint presentation]] in class during the final exam period on '''Tuesday, December 15, 2:00pm'''.
* Final due date for all other deliverables is no later than '''Friday, December 18, 4:30pm''' (according to official final exam schedule for fall, 2015).
* The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on digital media to either Dr. Dahlquist or Dr. Dionisio.
* Each member of the group will be assigned the same grade for the group project.
* Detailed specifications, particularly for the [[Gene Database Project Deliverables#Group Report|group report]] and [[Gene Database Project Deliverables#Individual Assessment and Reflection|individual assessment and reflection]], are given on the [[Gene Database Project Deliverables]] page.

=== Group Deliverables ===

* 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]]
** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:GenMAPP_schema_generic_bacteria_20151210.zip | GenMAPP_schema_generic_bacteria_20151210.zip]] 
*** Sample schema in jpeg format: [[Media:GenMAPP_schema_generic_bacteria_20151210.jpg | GenMAPP_schema_generic_bacteria_20151210.jpg]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=== Individual Deliverable ===

The individual deliverable is an [[Gene Database Project Deliverables#Individual Assessment and Reflection|assessment and reflection]] on the 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 and combined annotated bibliography (midnight 11/10)
* [[Week 11]] (midnight 11/17)
* [[Week 12]] (midnight 11/24)
* [[Week 14]] (midnight 12/8)
* [[Week 15]] (midnight 12/15)

== Groups ==

The project groups are:
# Team 1 - '''''Heavy Metal HaterZ''''' ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
#* Project Manager: Ron Legaspi
# Team 2 - '''Class Whoopers''' ''Bordetella pertussis'' (Whooping Cough)
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
#* Project Manager: Nicole Anguiano
# Team 3 - '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
#* Project Manager: Anu Varshneya
# Team 4 - ''' Oregon Trail Survivors''' ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristin Zebrowski
#* Project Manager: Kristin Zebrowski

== 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 (see above).

=== [[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). His or her tasks generally correspond to the work done during the DNA microarray analysis exercise ([http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1], [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]), as applicable to the team’s chosen bacterium.

=== [[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, Microsoft Excel, 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, version control, some troubleshooting, some programming. He or she coordinates with Drs. Dahlquist and Dionisio in extending GenMAPP Builder code and making new versions. GenMAPP Builder is written in Java and is built on open source pure-Java libraries. Source code is hosted on GitHub and built using Apache’s ''ant'' utility.

== 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.png|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://geneontology.org/page/download-ontology#Legacy_Downloads 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]]

{{Gene Database Project Links}}

[[Category:Group Projects]]

Gene Database Project Deliverables

2015-12-10T23:50:19Z

Kdahlquist: /* Group Files and Datasets */ generic schema in jpeg format

{{Gene Database Project Links}}

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

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

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== 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:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
</gallery>

* 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 from your [[Week 11|journal club outline and presentation]].
* 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.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.
# 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 a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
* Gene Database Schema figure
* Gene Database Testing Report on final version of Gene Database (can be put at the end of the report as an Appendix)
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
*** Write a paragraph interpreting the GO results in light of the experiment performed in the published paper.
** 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.
** In particular, compare directly the log fold change value of a couple of key genes mentioned in the paper with what you found for those genes.
** Compare the criteria the journal article used for a significant expression change to the criteria that you used. How many genes met the criterion for the article vs. how many met the criterion for your analysis.

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings.
* How closely do your findings correspond to the original study?
* Are there significant differences?
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 18 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
# Background on your species and your species' genome from the genome paper presentation.
# The results of the Gene Database creation
#* Gene Database Schema figure
#* A table that summarizes how many OrderedLocusNames IDs were found
#** by XMLPipeDB match in the UniProt XML file
#** by TallyEngine in the UniProt XML file
#** by TallyEngine in the PostgreSQL database
#** in the OriginalRowCounts table in the gdb
#** in your external model organism database source
#* Give the command used in match to generate these results
#* Give the query used in PGAdmin III to generate these results
#* Include a screenshot of the TallyEngine results as a figure
#* Report on quantity and identity of gene IDs that did not make it into the database
#*# OrderedLocusNames IDs that were not in the XML source at all
#*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
#*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
#* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
# Introduce the experiment performed in the microarray paper, including the experimental design flow chart
# Report results of the DNA microarray analysis
#* Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
#* Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
#* Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
#** Show a list of 15-20 non-redundant GO terms.
#** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
#* GenMAPP MAPP of a pathway relevant to your results
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, December 15.'''''
** 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 evaluated by the instructors using the [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Group Files and Datasets ==

* 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]]
** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:GenMAPP_schema_generic_bacteria_20151210.zip | GenMAPP_schema_generic_bacteria_20151210.zip]] 
*** Sample schema in jpeg format: [[Media:GenMAPP_schema_generic_bacteria_20151210.jpg | GenMAPP_schema_generic_bacteria_20151210.jpg]]
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

== 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 or as a Word document uploaded to your group deliveables 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?

{{Gene Database Project Links}}

[[Category:Group Projects]]

File:GenMAPP schema generic bacteria 20151210.jpg

2015-12-10T23:49:23Z

Kdahlquist: generic bacterial schema in jpeg format

generic bacterial schema in jpeg format

Gene Database Project Deliverables

2015-12-10T23:48:14Z

Kdahlquist: /* Group Files and Datasets */ changed out vibrio schema for generic one

{{Gene Database Project Links}}

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

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

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== 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:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
</gallery>

* 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 from your [[Week 11|journal club outline and presentation]].
* 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.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.
# 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 a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
* Gene Database Schema figure
* Gene Database Testing Report on final version of Gene Database (can be put at the end of the report as an Appendix)
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
*** Write a paragraph interpreting the GO results in light of the experiment performed in the published paper.
** 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.
** In particular, compare directly the log fold change value of a couple of key genes mentioned in the paper with what you found for those genes.
** Compare the criteria the journal article used for a significant expression change to the criteria that you used. How many genes met the criterion for the article vs. how many met the criterion for your analysis.

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings.
* How closely do your findings correspond to the original study?
* Are there significant differences?
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 18 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
# Background on your species and your species' genome from the genome paper presentation.
# The results of the Gene Database creation
#* Gene Database Schema figure
#* A table that summarizes how many OrderedLocusNames IDs were found
#** by XMLPipeDB match in the UniProt XML file
#** by TallyEngine in the UniProt XML file
#** by TallyEngine in the PostgreSQL database
#** in the OriginalRowCounts table in the gdb
#** in your external model organism database source
#* Give the command used in match to generate these results
#* Give the query used in PGAdmin III to generate these results
#* Include a screenshot of the TallyEngine results as a figure
#* Report on quantity and identity of gene IDs that did not make it into the database
#*# OrderedLocusNames IDs that were not in the XML source at all
#*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
#*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
#* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
# Introduce the experiment performed in the microarray paper, including the experimental design flow chart
# Report results of the DNA microarray analysis
#* Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
#* Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
#* Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
#** Show a list of 15-20 non-redundant GO terms.
#** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
#* GenMAPP MAPP of a pathway relevant to your results
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, December 15.'''''
** 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 evaluated by the instructors using the [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Group Files and Datasets ==

* 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]]
** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:GenMAPP_schema_generic_bacteria_20151210.zip | GenMAPP_schema_generic_bacteria_20151210.zip]] 
* Gene Database Testing Report for final submitted Gene Database (print from wiki to ''.pdf'' file)
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

== 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 or as a Word document uploaded to your group deliveables 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?

{{Gene Database Project Links}}

[[Category:Group Projects]]

File:GenMAPP schema generic bacteria 20151210.zip

2015-12-10T23:47:23Z

Kdahlquist: generic schema for a bacterial species including EnsemblBacteria as a system. Zipped .ai file

generic schema for a bacterial species including EnsemblBacteria as a system. Zipped .ai file

Heavy Metal HaterZ Files

2015-12-09T23:22:17Z

Kdahlquist: /* Statistical Analysis Excel Sheets */ link to edited file

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting KD.xlsx

2015-12-09T23:20:40Z

Kdahlquist: corrected Emily's file because there are 5408 genes, not 5409.

corrected Emily's file because there are 5408 genes, not 5409.

Main Page

2015-12-08T00:10:13Z

Kdahlquist: /* Announcements */ deleted old seminar announcements

__NOTOC__
<div style="text-align: center; font-size: 175%">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''BIOL/CMSI 367-01: Biological Databases'''</div>
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Fall 2015</div>

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

== Announcements ==

* The Microsoft Excel portion of the ID investigation protocol has been added to the wiki: [[Using Microsoft Excel to Compare ID Lists]]. The link has also been added to the course schedule below for Week 9.
:Please note that this version is similar, but not identical, to the process shown in class ([[User:Dondi|Dondi]] misremembered the function to use; it was supposed to be <code>match</code>, as shown in the wiki page, and not <code>lookup</code>). Furthermore, instructions for exporting from PostgreSQL (you might recall that the numbers did not match there either) are included. —''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:49, 29 October 2015 (PDT)''
* An initial round of feedback to the [[Week 6]] assignment has been posted to your respective user talk pages. The database part is not finished, but I figured some feedback and basics on the best practice stuff will be useful as you prepare your [[Week 8]] work (as in, get used to making the best practices routine so you can avoid nagging deductions week after week). —''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:30, 25 October 2015 (PDT)''
* To report issues with the configuration of the computers in Seaver 120, please record it on [[Talk:Software_Configuration | this wiki page.]] The complete list of software that should be installed for this course is found [[Software Configuration | here]]. Note that this configuration is Windows-specific. Some software may not be available for a Mac or may look differently.

=== Upcoming Seminars ===

* There are no more seminars for the rest of the semester.



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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User: Malverso | Mary Alverson]]
| style="padding-right: 1em" | [[User:Rlegaspi | Ron Legaspi]]
| style="padding-right: 1em" | [[User:Troque | Trixie Roque]]
| style="padding-right: 1em" | [[User:Jwoodlee | Jake Woodlee]]
|-
| style="padding-right: 1em" | [[User:Nanguiano | Nicole Anguiano]]
| style="padding-right: 1em" | [[User:Blitvak | Brandon Litvak]]
| style="padding-right: 1em" | [[user:Msaeedi23 | Mahrad Saeedi]]
| style="padding-right: 1em" | [[User:Kwyllie | Kevin Wyllie]]
|-
| style="padding-right: 1em" | [[User:Bklein7 | Brandon Klein]]
| style="padding-right: 1em" | [[User:Lenaolufson | Elena Olufson]]
| style="padding-right: 1em" | [[User:Emilysimso | Emily Simso]]
| style="padding-right: 1em" | [[User:Eyanosch | Erich Yanoschik]]
|-
| style="padding-right: 1em" | [[User:Jkuroda | Josh Kuroda]]
| style="padding-right: 1em" | [[User:Vpachec3 | Veronica Pacheco]]
| style="padding-right: 1em" | [[User:Anuvarsh | Anindita Varshneya]]
| style="padding-right: 1em" | [[User:Kzebrows | Kristin Zebrowski]]
|}

{{ Gene Database Project Links }}

== 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 Tuesdays at midnight (Monday night/Tuesday 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 office hours ({{ Dondi Office Hours }}) can be viewed as unofficial lab sessions: use them for IT help or desktop support

=== Part 1: Building Blocks (Genetic Code and Manipulating Text) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>9/1/2015
|
| 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

| rowspan="2" | [[Week 1]]

(due at midnight 9/8)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>9/3/2015
|
[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/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/8/2015
| [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)]

| DNA
* DNA structure and Genetic Code
* [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&content_id=_1103141_1 Slides shown in class on MyLMU Connect]
| rowspan="2" | [[Week 2]]

(due at midnight 9/15)

[[Class Journal Week 2]]
|-
!
| Thursday<br/>9/10/2015
| On [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset MyLMUConnect]:

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

Kaji & Kaji (2004) ''Setting the Record Straight''

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

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

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]
| 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.
* Slides shown in class
* [[Media:BIOL367_Fall2015_GeneticCode-GeneExpression.pdf | Genetic Code-Gene Expression Pencil Exercise]]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/15/2015
| [http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford (2015) ''What is Code?'']
* Emphasis on first two sections (“The Man in the Taupe Blazer” and “Let’s Begin”), but feel free to read further

[http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| An overview of computers, networks, files, and databases
* Useful help resource: http://explainshell.com
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| rowspan="2" | [[Week 3]]

(due at midnight 9/22)

[[Class Journal Week 3]]
|-
!
| Thursday<br/>9/17/2015
|
| Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/22/2015
| [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset 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/43/D1/D1.full Introduction to ''NAR'' Database Issue]

[http://scienceblogs.com/digitalbio/2015/01/30/bio-databases-2015/ Commentary on ''NAR'' Database Issue]

| Genome sequencing and annotation

Introduction to biological databases
* [https://mylmuconnect.blackboard.com/bbcswebdav/pid-1146580-dt-content-rid-1944592_1/courses/M_46692.201530/20150922_HGP_IntroBiolDB.pdf 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]
| rowspan="2" | [[Week 4]]

(due at midnight 9/29)

[[Class Journal Week 4]]
|-
!
| Thursday<br/>9/24/2015
| [[More Text Processing Features]]

[[How to Read XML Files]]
| Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion


{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/29/2015
| [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]

| 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/
| rowspan="2" | [[Week 5]]

(due at midnight 10/6)

[[Class Journal Week 5]]
|-
!
| Thursday<br/>10/1/2015
| 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).
| SQL and working with relational databases continued
* [[PostgreSQL Tutorial]]

{{Course Schedule Divider}}
|-
! style="background-color: #ddf" | 6
| style="background-color: #eef; border: none" | Tuesday<br/>10/6/2015
| style="background-color: #eef; border: none" |
| style="background-color: #eef; border: none" | President Synder’s Inauguration Day
| rowspan="2" | [[Week 6]]

(due at midnight 10/13)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/8/2015
|
| Database presentations
# Nicole, Erich, Kristen, Josh
# Mary, Emily, Brandon L., Kevin
# Lena, Jake, Anu, Veronica
# Ron, Mahrad, Brandon K., Trixie

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]

|}

=== Part 2: Going Deeper (Gene Expression Data and Relational Databases) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/13/2015
| [http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]

[http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

Campbell & Heyer Chapter 4 (on [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1 MyLMU Connect])

DeRisi et al. (1997) [http://www.sciencemag.org/content/278/5338/680.full ''Science'' 278: 680-686.]

| Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder
* [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&content_id=_1103141_1 Slides on MyLMU Connect]
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]
* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]

| rowspan="2" | [[Week 7]]

(due at midnight 10/20)

[[Class Journal Week 7]]
|-
!
| Thursday<br/>10/15/2015
| [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
| [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/]

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/20/2015
| [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']

[http://www.genomebiology.com/content/4/1/R7 Doniger et al. (2003) "MAPPFinder" ''Genome Biology'']
| [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis activity part 2]
| rowspan="2" | [[Week 8]]

(due at midnight 10/27)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/22/2015
|
| 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]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/27/2015
|
|
* Introduction to XMLPipeDB: export a Gene Database for ''Vibrio cholerae''
** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Group requests due midnight Saturday, October 31
| rowspan="2" | [[Week 9]]

(due at midnight 11/3)

[[Class Journal Week 9]]
|-
!
| Thursday<br/>10/29/2015
| [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'']
|
Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Using Microsoft Excel to Compare ID Lists]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
|}

=== Part 3: Integrating for Research (Gene Database Project) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 10
| Tuesday<br/>11/3/2015
|
|
* Annotated bibliography of genomics papers for your species
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
** Select genome paper for journal club
** Select microarray paper
| rowspan="2" | [[Week 10]]

(due at midnight 11/10)


|-
!
| Thursday<br/>11/5/2015
|
| Begin [[Gene_Database_Project | group projects]]

{{Course Schedule Divider}}
|-
! 11
| Tuesday<br/>11/10/2015
|
| Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| rowspan="2" | [[Week 11]]

(due at midnight 11/17)
|-
!
| Thursday<br/>11/12/2015
|
|

* Status report
* Work session

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/17/2015
|
| First Set of Journal Club Presentations
# Emily Simso/Ron Legaspi (Heavy Metal HaterZ)
# Anu Varshneya/Brandon Litvak (GÉNialOMICS)
# Lena Olufson/Mahrad Saeedi (Class Whoppers)
# Kristin Zebrowski and Erich Yanoschik (Oregon Trail Survivors)

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| rowspan="2" | [[Week 12]]

(due at midnight 11/24)

|-
!
| Thursday<br/>11/19/2015
|
|
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/24/2015
|
| Second Set of Journal Club Presentations
# Kevin Wyllie and Veronica Pacheco
# Brandon Klein (Class Whoopers)
# Mary Alverson and Josh Kuroda
# Jake Woodlee/Trixie Roque (Oregon Trail Survivors)

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| '''''No Week 13 assignment'''''

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/26/2015
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>12/1/2015
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at midnight 12/8)
|-
!
| Thursday<br/>12/3/2015
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/8/2015
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at midnight 12/15)
|-
!
| Thursday<br/>12/10/2015
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/15/2015
| style="background: #fee; border: none" |
| style="background: #fee; border: none" | '''Final project presentations 2:00-4:00 PM'''
| style="background: #fee; border: none" |
|-
!
| Friday<br/>12/18/2015 4:30 PM
|
| '''Project deliverables due 4:30 PM'''
|
|}

== 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:''' Life Sciences Building 289
: '''Office Hours:''' Tuesdays 9:00-11:00 AM, Wednesdays 1:30-3:30 PM and by appointment. I keep a sign-up sheet on my office door to facilitate appointment-making.

==== [[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:''' {{Dondi Office Hours}}

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in the Seaver College of Science and Engineering. 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 2:40–3:55pm, Seaver 120 

This is a hands-on, participatory course, thus attendance at all class meetings is required. Each student is allowed two “sick” days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 5% deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. 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 September 4. The withdrawal or credit/no-credit status deadline is November 6.

=== 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 ===

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

# As an LMU Lion, by the [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Lion%27s%20Code.pdf 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.
# You are responsible for your own learning and for being a good class citizen.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
# 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 away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises; however, if they are being used for other purposes and become distracting to you or others, you will be asked to put them away.
# All students are governed by [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Loyola-Marymount-University-Community-Standards-2015-2016.pdf LMU Community Standards Publication]. 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.

=== Course Website ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2015/. You will need to [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php?title=Special:UserLogin&returnto=Main+Page&type=signup 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 [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset BIOL/CMSI 367-01 on MyLMUConnect]. The two cross-listed sections are using the same site, which is listed as "Biological Databases Fall 2015" with no department or course number. The MyLMUConnect site will be used for materials that cannot be made public on this wiki, including grades.

=== E-mail Communication ===

At times we will communicate with the entire class using campus e-mail systems, so it is essential that you regularly check your lion.lmu.edu e-mail address or forward your lion account e-mail to your preferred e-mail address. Messages sent to the instructors at night or on the weekend will be answered the next school day. Please CC both instructors on all e-mail messages related to this class.

=== 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 this wiki or the 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
* [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Special:UserLogin/signup Account for this wiki]
* [https://secure.cs.lmu.edu/ Computer Science account]
* [http://www.github.com GitHub 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-to-day 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

==== University Core Curriculum ====

This course fulfills the following requirements in the University Core Curriculum:
* Integrations: Interdisciplinary Connections
* Upper Division Information Literacy Flag
* Upper Division Oral Communication Flag

=== 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 five 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, individual (10 points each)
| style="text-align: right" | 140
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (3 points each)
| style="text-align: right" | 42
| points
|-
| Oral presentations
| style="text-align: right" | 105
| points 
|-
| Information literacy (additional points added to two journal assignments)
| style="text-align: right" | 24
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''486'''
| '''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 Tuesday PST (''Monday night/Tuesday morning''); consult the schedule for specific due dates for each assignment.
* Each weekly assignment has an individual component and a shared component. You will earn 10 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry. '''''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 on your user talk pages.
* 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:
** Your electronic laboratory notebook and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning
* For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).

==== 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 and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.'''''

==== Final Group Project ====

{{ Gene Database Project Links }}

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, specifically [https://peerj.com/computer-science/ PeerJ Computer Science]. Specific instructions are posted [[Gene Database Project Deliverables|here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 18 at 4:30 PM. The Final Written Report must be completed to receive a passing grade in the course.'''''

==== Extra Credit ====

Students may accumulate up to 12.5 points toward 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 2.5 points with up to 5 seminars (12.5 points) 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 '''''hard copy''''' of your summary of the seminar '''''in class, within one week''''' of the date of the seminar or they will not count as extra credit.

=== 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.

=== 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.” Attempting to gain extra credit for a seminar that you did not attend or assisting another student to do this are examples of academic dishonesty and will be considered a violation of the Honor Code. [http://bulletin.lmu.edu/content.php?catoid=6&navoid=250#LMU_Honor_Code_and_Process 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:BIOL367_Fall2015_HonorCodeAgreement.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/content.php?catoid=6&navoid=250#LMU_Honor_Code_and_Process LMU Honor Code and Process].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [[Media:Avoiding_plagiarism.pptx | Academic Resource Center presentation on plagiarism]] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Americans with Disabilities Act—Special Accommodations ===

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/fall2015/.

User talk:Rlegaspi

2015-12-08T00:07:51Z

Kdahlquist: uploaded file and sent instructions

== 2015-12-07 ==

* A new file with the split data has been uploaded to your team's files page: UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx
** Note that this file is based on "UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH.xlsx". I still found an error in the other version of the file that there was a gene called "Gene ID" on the CompiledRawData sheet. This led to a missing gene on the MasterSheet and a discrepancy in the data for the scaling and centering between the two files in the fourth decimal place.

You now need to do the following:
# Average together the replicate data from the two spots that are now split. This means that you need to average the "Log2FC-C0-rep1-scaledandcentered" in cell C2 with the value in cell AG2, for example.
# Copy and paste special > paste values into a new sheet called "statistics".
# Compute the average of the biological replicates for each treatment and timepoint. For example, average together all four biological replicates for Log2FC-C0. Repeat for each timepoint.
# Compute the ratio of the average log ratios so that you have values for the Average Log Ratio of C5/C0, C20/C0, C60/C0, F5/C60, F20/C60, and F60/C60). Since this is in log space, to take the ratio, you will actually subtract instead of divide.
# Perform a two-sample T test between C5 and C0, C20 and C0, C60 and C0, F5 and C60, etc. Use the equation:
=TTEST(<range of cells containing the biological replicates for C0>, <range of cells containing the biological replicates for C5>, 2,3]
: This will return the p value. Send me the link to the file at this point so I can check the results. You can also perform the sanity check. Let me know how it goes.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:07, 7 December 2015 (PST)''

== 2015-12-04 Discrepancies between partner data ==

Hi Ron and Emily,

I've spent some more time looking at the files you both sent me and there are multiple issues that need to be addressed before we can move on with the analysis.

# Emily, the contents of your most recent file I downloaded don't seem to match the one that I used to split your data. For example, in the old file, in the CompiledRawData, MasterSheet, and ScalingCentering sheets, it had data from the C1, C5, C20, and C60 timepoints, but the new file has data for F1, F5, F20, and F60, which is extremely odd.
# The total set of timepoints that you need are C0, C5, C20, C60, F5, F20, and F60. This means that you don't need C1 and that you need to add C0 and that you don't need F1. It appears that Ron's data has the correct set of timepoints in his CompiledRawData sheet. However, there are other issues that need to be addressed.
# In the CompiledRawData sheet you both have 11520 genes. The very last gene in Ron's sheet has the phrase "Gene ID" instead of the actual ID, which should be SO4357, according to Emily's data. Then in the next sheet called MasterSheet, then Ron's data is missing one row, presumably because he deleted the row with "Gene ID" as the ID. You need to recover that data.
# When I actually looked at the numerical data for what should have been the LogFC for the same treatment, timepoint, and replicate, the data does not match between Ron and Emily.

Before we can go any further, we need to sort out these discrepancies and come up with a consistent set of data that you both can work on. The two of you need to get together and do the following:

* Re-create the CompiledRawData sheet with the C0, C5, C20, C60, F5, F20, and F60 data and with all of the correct IDs. You need to come up with one consistent set of data for the log fold changes so that you are each not working on different values. It is clear that there are differences in how you each computed the log fold changes and you need to decide which set of numbers to proceed with.
* You just need to recreate the CompiledRawData sheet at this point. When you have that, please upload it to the wiki and send me the link. By the way, you should be linking these files to your team's file page so I can just go there to find them. Please name this new file something different than the previous files you have both worked on. I will process it to the splitting step at this point myself and send it back to you when I've done that.
* There were some further issues with the calculations that Emily did after that point, but I will address that once we have a CompiledRawData sheet that we know is correct.

There is the possibility that I can be online tonight after ~9:30PM, so if you can send me something by then I could potentially look at it tonight. My next window of opportunity is tomorrow at 2:00 PM. To get on track with what needs to be done, it would be really good to try and get me something by tomorrow. If that's not really possible, Sunday at 2:00 is my next window.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:15, 4 December 2015 (PST)''

== Week 12 Feedback ==

* I have reviewed the work that Emily and you did to compile your raw data this last week and want to acknowledge the hard work that you both put in to organize the files and perform the calculations. I'm putting the feedback here on your page and will put a note on Emily's talk page to refer her to this page.
* In light of the effort that it took to get to this point and to cut down on the additional workload that your particular dataset entails, from this point forward, let's cut out two of the timepoints for the depletion and repletion experiments (ignoring the 10 minute and 40 minute timepoints and keeping the 0, 5, 20, and 60 minute timepoints).
*# All of your calculations at this point exist as individual files; you need to compile all of the log ratios you computed into a single file. In a new workbook, name the first sheet "CompiledRawData". Name Column A "ID" and copy and paste in the list of IDs from one of your files.
*# Create a "MasterIndex" column as follows. Insert a new column to the right of the "ID" column and name it "MasterIndex". In this column you will create a numerical index of genes so that you can always sort them back into the same order that they started out in.
*#* Type a "1" in cell B2 and a "2" in cell B3.
*#* Select both cells. Hover your mouse over the bottom-right corner of the selection until it makes a thin black + sign. Double-click on the + sign to fill the entire column with a series of numbers from 1 to 11520 (the number of spots on the microarray).
*# Then you need to copy and paste (values) the "log2" column from your individual files. They should be in order Log2FC-CO-rep1, Log2FC-CO-rep2, Log2FC-C0-rep3, Log2FC-C0-rep4, Log2FC-C5-rep1, etc.
*# The next set of manipulations should be performed in a new sheet called "MasterSheet".
*# Sort the data A-->Z based on the "ID" column. Delete all rows that have an ID of "Blank", "blank", "gDNA", start with "NC-", start with "ORF". Record how many rows got deleted.
*# Some of your cells are going to have error messages in them because of the previous calculations you did. Find and replace all of these with nothing, record how many cells that is.
*# Create a new worksheet called "ScalingCentering" and copy and paste special all of your data into this new sheet. [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae#Normalize_the_log_ratios_for_the_set_of_slides_in_the_experiment You will perform the scaling and centering operations like you did for the ''Vibrio cholerae'' data.]
*#* Once you have done this, e-mail Dr. Dahlquist and provide a link to your file. Your microarray data has duplicated spots. I have a script that will separate these out so that you can average them as technical replicates.
*# Create a new worksheet called "Statistics", copy and paste the values into this new sheet.
*# You will average the technical replicate spots for each sample to get one value for each sample.
*# You will average the biological replicates for each timepoint to get an average for each timepoint (C0, C5, C20, C60, F5, F20, F60).
*# You will take the ratio of the average log ratios so that you have values for the Average Log Ratio of C5/C0, C20/C0, C60/C0, F5/C60, F20/C60, and F60/C60). Since this is in log space, to take the ratio, you will actually subtract instead of divide.
*# You will perform a two-sample T test between C5 and C0, C20 and C0, C60 and C0, F5 and C60, etc. and perform the Bonferroni and Benjamini and Hochberg corrections on these p values. This computation is not the same as what we did for ''Vibrio''. Instead you will use the <code>TTEST</code> function in Excel (see me when you are ready to do this). The corrections will be the same as what you did before.
*# After that, then you will need to then format the data for GenMAPP and you'll be ready to import it into GenMAPP and run MAPPFinder.
* Let me know if you have any questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:34, 24 November 2015 (PST)''

== Week 6 Feedback ==

I’ve chosen to issue partial feedback sooner than complete feedback later, in case it will help you address issues with [[Week 8]].

=== Best Practices ===

* Individual work was submitted on time.
* Shared work was not submitted at all.
* Requisite links to and from the user page as well as page categories are all present.
* Electronic notebook was partially maintained, but not finished: the section where you supply the <code>sed</code> command sequences for preparing the data files is provided without any notes, yet there is an indication (“Explanation here.”) indicating you had something to say. You should record your notebook ''as you work'' so that you can avoid missing these in the end.
* Work was submitted in appropriate frequencies with corresponding summaries.

=== Database Exercises ===

Work in progress.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:19, 25 October 2015 (PDT)''

== Week 4 Feedback ==

* Individual work was not submitted on time, with the final edit landing at 12:48pm on 9/29.
* Good-habit items are mostly fulfilled:
** All expected links and categories were noted.
** Electronic notebook content was seen, but detail drops off significantly in the second and third questions.
** Summaries were consistently provided over a good number of edits, with notably detailed descriptiveness.
* For the exercises, the following issues were seen; all others were correct:
** A consistent typo appears in all of your answers: the correct notation for six repeated symbols is <code>(.){6}</code>, and not <code>(.)6</code> as submitted. This caused some initial issues when I was checking your work because I had to track down the offending command.
** Another consistent typo appears in the command sequence from the stop codon onward: there is a missing space in the line break substitution after the <code><\/start_codon></code> pattern. This breaks all subsequent output if the command sequence is run as-is. Again, a lot of effort went into tracking down the problem. Absolute precision is needed when transcribing from the command line into the wiki.
** There is an inconsistency in your mRNA answer (which also manifests the aforementioned typo): your previous answer on the transcription start site is correct, and the command supplied with your mRNA answer is also correct (assuming the typo is fixed), but the output you provide shows the wrong transcription start site. Now, given that there is insufficient detail in the lab notebook portion here, it cannot be determined whether this was just a typing/copy-paste error, a coding mistake, or some other issue. This is why an electronic notebook is valuable.
** Your translation answer also exhibits significant transcription problems. Not only are the previous typos present, but the deletion portion in the end (second- and third-to-last lines) shows distinct overlap and redundancy, plus there is a missing pipe symbol (<code>|</code>) on the 9th line. Again, the lack of electronic notebook commentary does not shed light on your full intent or understanding of these commands, and this once more hurts the quality of your answer.
* Shared responses were provided and they came in on time.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:59, 7 October 2015 (PDT)''

== Week 3 Feedback ==

* Individual work was submitted on time, but not enough time remained to finish the shared journal entry on time. Yes, it was only late by 26 seconds, but see what you can do about giving yourself greater margin for error.
* Aside from punctuality all other good-habit items are fulfilled:
** All expected links and categories were noted.
** You were able to phase your work well, and consistently supplied a change summary to all of them.
** You accompanied your work with electronic notes and processes.
* What follows is my feedback for the answers you provided:
** Complement was exactly right.
** Your 6 reading frames produced the right result, but not in the best way. Specifically, to “clean up” the remaining base pairs, you “pre-cut” them from the end. This does produce the correct result but requires foreknowledge of exactly how long the nucleotide sequence is. What if you were given a gene consisting of thousands of bases? There is a way to process the sequences without having to know how many bases to “chop” at the end.
** All of your ''xmlpipedb-match'' answers were correct except for the last one. The difference in numbers did not have to do with capitalization, but something else. I will it at that for now to give you an opportunity to figure it out initially. If you want to know directly, just ask me.
* Your initial experiences with the command line definitely reflect what many others experience when they learn this new approach to interacting with a computer. Keep at it and keep practicing. Repetition helps here, and, as you wrote, gradual expansion of your understanding of each command is also worth consciously building toward. Fortunately there are many resources on the Internet, calibrated for various skill levels, available to help you in this area.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:35, 26 September 2015 (PDT)''

== Week 2 Feedback ==

* Although, the [[Week 2]] scores have not yet been posted, I want to give you feedback on the assignment that you can incorporate to your your [[Week 3]] submission.
* First, thank you for submitting your assignment on time.
* Your translations are correct.
* You did not include anything by the way of an electronic notebook for this assignment. Although this assignment was pretty straightforward, you still need to document the process of what you did to arrive at the answers, not just supply the answers. Please be sure to do this for your Week 3 submission.
* You wrote something in the Summary field for 35/35 contributions between the Week 1 and Week 2 deadlines, keep up the good work!
* You did include the category on your individual journal entry. However, you should actually put this on your template page, instead of adding it separately to the journal entry page. This way, you will never forget to add it as long as you invoke your template on your journal entry page.
* With regards to your comments on your shared journal entry, as you can see, others found the Kaji and Kaji article difficult to understand. It's often the shortest scientific articles that are the most difficult!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:17, 18 September 2015 (PDT)''

== Week 2 Feedback Response ==
* Thank you for your feedback Dr. Dahlquist.
* I will definitely include an "electronic notebook" for the Week 3 assignment and I will also include one for the Week 2 assignment since I have the work I did on paper.
* I will fix my template to include the categories for the the assignments from here on out.
* Week 3 assignment is a bit more tricky since I'm not acquainted with code and the command line, but Prof. Dionisio did a good job of explaining a lot of commands and will attempt to finish the individual assignment by the end of tonight.

''— [[User:Rlegaspi|Rlegaspi]] ([[User talk:Rlegaspi|talk]]) 17:19, 20 September 2015 (PDT)

----

== Week 1 Feedback ==

* I answered your question on my [[User_talk:Kdahlquist | User talk page.]]
* The scores have not been posted yet, but I wanted to give you feedback on your [[Week 1]] Assignment.
* Your individual assignment was late (submitted at 03:01), your questions on our talk pages were late (submitted at 02:38 and 02:42), and your shared assignment was late (submitted at 02:45). In the future, make sure to give yourself enough time to complete the assignment so that you do not submit your work late.
* Your assignment is complete except for the items that I list below. I particularly like how you took advantage of external links in your work history and other areas of your page. Your work history could be improved by making further sub-bullets after you give the location and dates of your employment. You wrote something in the Summary field 100% of the time, good work!
* Missing items:
*# You did not send an e-mail to myself and Dr. Dionisio answering the questions whether you had any concerns or whether there was anything else you wanted us to know. Please e-mail us with your answers, even if your answers are "no".
*# You need to upload an image and use it on your page.
*# You need to upload another type of file and link to it on your page.
* You will have the opportunity to make up some of the points you missed by completing the tasks listed above by the [[Week 2]] deadline, midnight on September 15.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:43, 8 September 2015 (PDT)''

== Week 1 Feedback Response ==

* Thank you for answering the question.
* I apologize for the late submissions. I didn't expect to work so much over the Labor Day Weekend and was only able to finish my page after the closing shift. I will upload an image of myself and a few images relating to the content on my page; in addition to another type of file.
* Again, I appreciate the feedback. I am going to do a better job of spreading out my tasks and staying true to my weekly study plan.

''— [[User:Rlegaspi|Rlegaspi]] ([[User talk:Rlegaspi|talk]]) 13:59, 8 September 2015 (PDT)

----

I’ve answered your question on my [[User_talk:Dondi | talk page]].

''—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:56, 12 September 2015 (PDT)''

Heavy Metal HaterZ Files

2015-12-07T23:47:03Z

Kdahlquist: /* Statistical Analysis Excel Sheets */ link to split data file

File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH forsplitting.xlsx

2015-12-07T23:45:53Z

Kdahlquist: split data is in sheet "SplitData"; workbook originated from the file UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH.xlsx downloaded on 2015-12-07

split data is in sheet "SplitData"; workbook originated from the file UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH.xlsx downloaded on 2015-12-07

User talk:Emilysimso

2015-12-05T00:16:53Z

Kdahlquist: link to Ron's page

== 2012-12-04 ==

I've posted the text of my e-mail on [[User_talk:Rlegaspi#Week_12_Feedback | Ron's User Talk page.]] ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:16, 4 December 2015 (PST)''

== Week 12 Feedback ==

I've posted feedback and instructions for what to do next on [[User_talk:Rlegaspi#Week_12_Feedback | Ron's User Talk page.]] ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 24 November 2015 (PST)''

== Week 6 Feedback ==

I’ve chosen to issue partial feedback sooner than complete feedback later, in case it will help you address issues with [[Week 8]].

=== Best Practices ===

* Individual and shared work were both submitted on time.
* Requisite links to and from the user page as well as page categories are all present.
* Electronic notebook was maintained.
* Work was submitted in appropriate frequencies with corresponding summaries.
* ''This amounts to a “best practices” perfect score. Good work, keep it up!''

=== Database Exercises ===

Work in progress.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:40, 25 October 2015 (PDT)''

== Week 4 Feedback ==

* Work was submitted 2 days early—now ''that’s'' time management!
* All good-habit items are fulfilled:
** All expected links and categories were noted.
** Electronic notebook content was seen.
** Summaries were consistently provided over 6 edits. That would be the one knock on the good-habit items—this assignment was sufficiently difficult so as to easily justify working in smaller chunks than you did.
* For the exercises, the following issues were seen; all others were correct:
** You were off by one nucleotide on the transcription start site.
** The incorrect stop codon was chosen.
** Complementation was not needed for the mRNA strand. Further, the actual command (beyond the complement, which was incorrect to do anyway) was not supplied.
** Because the mRNA was incorrect, then the resulting amino acid sequence was incorrect as well. Further, translation must only happen between start and stop codons inclusive. Finally, the intent of the exercise is a fully automated command sequence, without the need for human typing in between.
* Shared responses were provided and they came in on time.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:53, 4 October 2015 (PDT)''

== Week 3 Feedback ==

* Work was submitted on time—keep it up!
* Nearly all good-habit items are fulfilled:
** All expected links and categories were noted.
** You were able to phase your work well, and consistently supplied a change summary to all of them.
** You provided some electronic notes alongside your answers but they could have been more detailed, especially for the responses where the full command sequences were not determined (see below). These details can elaborate your intent or what you wanted the command to do, and can illuminate areas where further explanation might be warranted.
* Feedback on your exercise responses is as follows:
** You got the complement right; small note, in your notes “complementary” was misspelled as “complimentary.” Understandable, but all the more reason to be vigilant for that.
** For the reading frames, you got partway through them but missed some key information from the readings. These were not explicitly shown in class, but could have been gleaned from the supplied wiki pages and/or by communicating with your homework partner:
*** Reading frames 2, 3, –2, and –3 need to “skip” either one or two bases from the beginning.
*** The ''genetic-code.sed'' file is crucial in being able to systematically convert ''all'' codons to their appropriate amino acids.
*** You found the need for the <code>rev</code> command for negative-direction reading frames, but missed that, being in the 3'-to-5' direction the complements would then be needed for correct transcription.
*** Please come to office hours or set an appointment so we can talk through these missed steps in greater detail.
** All responses for the ''xmlpipedb-match'' exercises are correct.
* Thank you for your shared responses. It is heartening to read that you are getting great support for your career choice at LMU, to counterbalance some of the questions raised by those from an earlier generation. Also noting that this is your first time with code, to echo the note above, let’s find some extra office hours time to get you a little more practice and exposure with this strange new way of interacting with a computer ''':)'''

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:30, 26 September 2015 (PDT)''

== Week 2 Feedback ==

* Although, the [[Week 2]] scores have not yet been posted, I want to give you feedback on the assignment that you can incorporate to your your [[Week 3]] submission.
* First, thank you for submitting your assignment on time.
* Your translations are correct; although it would have been better for completeness to go ahead and translate the rest of the sequence after the stop codon, in this case.
* You did not include anything by the way of an electronic notebook for this assignment. Although this assignment was pretty straightforward, you still need to document the process of what you did to arrive at the answers, not just supply the answers. Please be sure to do this for your Week 3 submission.
* You wrote something in the Summary field for 26/26 contributions between the Week 1 and Week 2 deadlines, keep up the good work!
* For each week's assignment, you will need to create links from your User page to that week's assignment and to your individual and shared journal entries, as well as a link back from your individual journal entry and to the category "Journal Entry".
** You are missing all of these on your [[Emilysimso Week 2]] page.
** However, all of these links, except for the link to your User page actually exist on your template, "Esimso entries etc". So all you have to do to remedy this situation is:
**# Add a link to your user page on your template.
**# '''''Invoke''''' your template on your week 2 journal entry page by using the syntax <nowiki>{{Esimso entries etc}}</nowiki>.
** You could even go ahead and create all of your future individual journal entry pages by invoking your template on them and never have to worry about losing points for this part of the assignment again.
* If you begin a line with a single space character, the text will appear in a fixed-width font, which is better for representing nucleic acid and protein sequences because they will then line up with each other better.
* With regards to your comments on your shared journal entry, the Nirenberg article is difficult because it is filled with experimental detail to which you may not have been previously exposed. However, I also think it's a good exercise to go back to the original source sometimes and read about discoveries from "the horse's mouth" so to speak.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:53, 18 September 2015 (PDT)''

== Week 1 Feedback ==

* I have answered your question on my [[User_talk:Kdahlquist | User talk page.]]
* Thank you for submitting your work on time.
* While the scores for the [[Week 1]] assignment have not yet been posted, I want to give you feedback on the assignment.
* You entered something in the Summary field 100% of the time. Keep up the good work!
* The following items are either missing or need to be tweaked:
*# You have a stray bullet point under the section describing your favorite aspect of computer science. This happened because you started your list with two asterisks without having a bullet point with just one.
*# You uploaded your resume as a file, but I suggest you change the filename to something with your name in it. Using a generic filename like you did makes it difficult for other people to keep track of your file and could be mistaken for someone else's file.
*# Please remove the "shared" category from your User page, because that page is not technically shared.
*# You have neither created nor used the template. Please let us know if you need assistance with this because you will want to use it for the rest of the semester.
* You will have the opportunity to make up the points that you missed on this assignment by making corrections by the [[Week 2]] journal deadline on midnight, September 15.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:12, 8 September 2015 (PDT)''

I’ve answered your question on my [[User_talk:Dondi | talk page]].

''—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:02, 11 September 2015 (PDT)''

User talk:Rlegaspi

2015-12-05T00:15:59Z

Kdahlquist: pasted in from e-mail

== 2012-12-04 Discrepancies between partner data ==

Hi Ron and Emily,

I've spent some more time looking at the files you both sent me and there are multiple issues that need to be addressed before we can move on with the analysis.

# Emily, the contents of your most recent file I downloaded don't seem to match the one that I used to split your data. For example, in the old file, in the CompiledRawData, MasterSheet, and ScalingCentering sheets, it had data from the C1, C5, C20, and C60 timepoints, but the new file has data for F1, F5, F20, and F60, which is extremely odd.
# The total set of timepoints that you need are C0, C5, C20, C60, F5, F20, and F60. This means that you don't need C1 and that you need to add C0 and that you don't need F1. It appears that Ron's data has the correct set of timepoints in his CompiledRawData sheet. However, there are other issues that need to be addressed.
# In the CompiledRawData sheet you both have 11520 genes. The very last gene in Ron's sheet has the phrase "Gene ID" instead of the actual ID, which should be SO4357, according to Emily's data. Then in the next sheet called MasterSheet, then Ron's data is missing one row, presumably because he deleted the row with "Gene ID" as the ID. You need to recover that data.
# When I actually looked at the numerical data for what should have been the LogFC for the same treatment, timepoint, and replicate, the data does not match between Ron and Emily.

Before we can go any further, we need to sort out these discrepancies and come up with a consistent set of data that you both can work on. The two of you need to get together and do the following:

* Re-create the CompiledRawData sheet with the C0, C5, C20, C60, F5, F20, and F60 data and with all of the correct IDs. You need to come up with one consistent set of data for the log fold changes so that you are each not working on different values. It is clear that there are differences in how you each computed the log fold changes and you need to decide which set of numbers to proceed with.
* You just need to recreate the CompiledRawData sheet at this point. When you have that, please upload it to the wiki and send me the link. By the way, you should be linking these files to your team's file page so I can just go there to find them. Please name this new file something different than the previous files you have both worked on. I will process it to the splitting step at this point myself and send it back to you when I've done that.
* There were some further issues with the calculations that Emily did after that point, but I will address that once we have a CompiledRawData sheet that we know is correct.

There is the possibility that I can be online tonight after ~9:30PM, so if you can send me something by then I could potentially look at it tonight. My next window of opportunity is tomorrow at 2:00 PM. To get on track with what needs to be done, it would be really good to try and get me something by tomorrow. If that's not really possible, Sunday at 2:00 is my next window.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:15, 4 December 2015 (PST)''

== Week 12 Feedback ==

* I have reviewed the work that Emily and you did to compile your raw data this last week and want to acknowledge the hard work that you both put in to organize the files and perform the calculations. I'm putting the feedback here on your page and will put a note on Emily's talk page to refer her to this page.
* In light of the effort that it took to get to this point and to cut down on the additional workload that your particular dataset entails, from this point forward, let's cut out two of the timepoints for the depletion and repletion experiments (ignoring the 10 minute and 40 minute timepoints and keeping the 0, 5, 20, and 60 minute timepoints).
*# All of your calculations at this point exist as individual files; you need to compile all of the log ratios you computed into a single file. In a new workbook, name the first sheet "CompiledRawData". Name Column A "ID" and copy and paste in the list of IDs from one of your files.
*# Create a "MasterIndex" column as follows. Insert a new column to the right of the "ID" column and name it "MasterIndex". In this column you will create a numerical index of genes so that you can always sort them back into the same order that they started out in.
*#* Type a "1" in cell B2 and a "2" in cell B3.
*#* Select both cells. Hover your mouse over the bottom-right corner of the selection until it makes a thin black + sign. Double-click on the + sign to fill the entire column with a series of numbers from 1 to 11520 (the number of spots on the microarray).
*# Then you need to copy and paste (values) the "log2" column from your individual files. They should be in order Log2FC-CO-rep1, Log2FC-CO-rep2, Log2FC-C0-rep3, Log2FC-C0-rep4, Log2FC-C5-rep1, etc.
*# The next set of manipulations should be performed in a new sheet called "MasterSheet".
*# Sort the data A-->Z based on the "ID" column. Delete all rows that have an ID of "Blank", "blank", "gDNA", start with "NC-", start with "ORF". Record how many rows got deleted.
*# Some of your cells are going to have error messages in them because of the previous calculations you did. Find and replace all of these with nothing, record how many cells that is.
*# Create a new worksheet called "ScalingCentering" and copy and paste special all of your data into this new sheet. [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae#Normalize_the_log_ratios_for_the_set_of_slides_in_the_experiment You will perform the scaling and centering operations like you did for the ''Vibrio cholerae'' data.]
*#* Once you have done this, e-mail Dr. Dahlquist and provide a link to your file. Your microarray data has duplicated spots. I have a script that will separate these out so that you can average them as technical replicates.
*# Create a new worksheet called "Statistics", copy and paste the values into this new sheet.
*# You will average the technical replicate spots for each sample to get one value for each sample.
*# You will average the biological replicates for each timepoint to get an average for each timepoint (C0, C5, C20, C60, F5, F20, F60).
*# You will take the ratio of the average log ratios so that you have values for the Average Log Ratio of C5/C0, C20/C0, C60/C0, F5/C60, F20/C60, and F60/C60). Since this is in log space, to take the ratio, you will actually subtract instead of divide.
*# You will perform a two-sample T test between C5 and C0, C20 and C0, C60 and C0, F5 and C60, etc. and perform the Bonferroni and Benjamini and Hochberg corrections on these p values. This computation is not the same as what we did for ''Vibrio''. Instead you will use the <code>TTEST</code> function in Excel (see me when you are ready to do this). The corrections will be the same as what you did before.
*# After that, then you will need to then format the data for GenMAPP and you'll be ready to import it into GenMAPP and run MAPPFinder.
* Let me know if you have any questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:34, 24 November 2015 (PST)''

== Week 6 Feedback ==

I’ve chosen to issue partial feedback sooner than complete feedback later, in case it will help you address issues with [[Week 8]].

=== Best Practices ===

* Individual work was submitted on time.
* Shared work was not submitted at all.
* Requisite links to and from the user page as well as page categories are all present.
* Electronic notebook was partially maintained, but not finished: the section where you supply the <code>sed</code> command sequences for preparing the data files is provided without any notes, yet there is an indication (“Explanation here.”) indicating you had something to say. You should record your notebook ''as you work'' so that you can avoid missing these in the end.
* Work was submitted in appropriate frequencies with corresponding summaries.

=== Database Exercises ===

Work in progress.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:19, 25 October 2015 (PDT)''

== Week 4 Feedback ==

* Individual work was not submitted on time, with the final edit landing at 12:48pm on 9/29.
* Good-habit items are mostly fulfilled:
** All expected links and categories were noted.
** Electronic notebook content was seen, but detail drops off significantly in the second and third questions.
** Summaries were consistently provided over a good number of edits, with notably detailed descriptiveness.
* For the exercises, the following issues were seen; all others were correct:
** A consistent typo appears in all of your answers: the correct notation for six repeated symbols is <code>(.){6}</code>, and not <code>(.)6</code> as submitted. This caused some initial issues when I was checking your work because I had to track down the offending command.
** Another consistent typo appears in the command sequence from the stop codon onward: there is a missing space in the line break substitution after the <code><\/start_codon></code> pattern. This breaks all subsequent output if the command sequence is run as-is. Again, a lot of effort went into tracking down the problem. Absolute precision is needed when transcribing from the command line into the wiki.
** There is an inconsistency in your mRNA answer (which also manifests the aforementioned typo): your previous answer on the transcription start site is correct, and the command supplied with your mRNA answer is also correct (assuming the typo is fixed), but the output you provide shows the wrong transcription start site. Now, given that there is insufficient detail in the lab notebook portion here, it cannot be determined whether this was just a typing/copy-paste error, a coding mistake, or some other issue. This is why an electronic notebook is valuable.
** Your translation answer also exhibits significant transcription problems. Not only are the previous typos present, but the deletion portion in the end (second- and third-to-last lines) shows distinct overlap and redundancy, plus there is a missing pipe symbol (<code>|</code>) on the 9th line. Again, the lack of electronic notebook commentary does not shed light on your full intent or understanding of these commands, and this once more hurts the quality of your answer.
* Shared responses were provided and they came in on time.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:59, 7 October 2015 (PDT)''

== Week 3 Feedback ==

* Individual work was submitted on time, but not enough time remained to finish the shared journal entry on time. Yes, it was only late by 26 seconds, but see what you can do about giving yourself greater margin for error.
* Aside from punctuality all other good-habit items are fulfilled:
** All expected links and categories were noted.
** You were able to phase your work well, and consistently supplied a change summary to all of them.
** You accompanied your work with electronic notes and processes.
* What follows is my feedback for the answers you provided:
** Complement was exactly right.
** Your 6 reading frames produced the right result, but not in the best way. Specifically, to “clean up” the remaining base pairs, you “pre-cut” them from the end. This does produce the correct result but requires foreknowledge of exactly how long the nucleotide sequence is. What if you were given a gene consisting of thousands of bases? There is a way to process the sequences without having to know how many bases to “chop” at the end.
** All of your ''xmlpipedb-match'' answers were correct except for the last one. The difference in numbers did not have to do with capitalization, but something else. I will it at that for now to give you an opportunity to figure it out initially. If you want to know directly, just ask me.
* Your initial experiences with the command line definitely reflect what many others experience when they learn this new approach to interacting with a computer. Keep at it and keep practicing. Repetition helps here, and, as you wrote, gradual expansion of your understanding of each command is also worth consciously building toward. Fortunately there are many resources on the Internet, calibrated for various skill levels, available to help you in this area.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:35, 26 September 2015 (PDT)''

== Week 2 Feedback ==

* Although, the [[Week 2]] scores have not yet been posted, I want to give you feedback on the assignment that you can incorporate to your your [[Week 3]] submission.
* First, thank you for submitting your assignment on time.
* Your translations are correct.
* You did not include anything by the way of an electronic notebook for this assignment. Although this assignment was pretty straightforward, you still need to document the process of what you did to arrive at the answers, not just supply the answers. Please be sure to do this for your Week 3 submission.
* You wrote something in the Summary field for 35/35 contributions between the Week 1 and Week 2 deadlines, keep up the good work!
* You did include the category on your individual journal entry. However, you should actually put this on your template page, instead of adding it separately to the journal entry page. This way, you will never forget to add it as long as you invoke your template on your journal entry page.
* With regards to your comments on your shared journal entry, as you can see, others found the Kaji and Kaji article difficult to understand. It's often the shortest scientific articles that are the most difficult!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:17, 18 September 2015 (PDT)''

== Week 2 Feedback Response ==
* Thank you for your feedback Dr. Dahlquist.
* I will definitely include an "electronic notebook" for the Week 3 assignment and I will also include one for the Week 2 assignment since I have the work I did on paper.
* I will fix my template to include the categories for the the assignments from here on out.
* Week 3 assignment is a bit more tricky since I'm not acquainted with code and the command line, but Prof. Dionisio did a good job of explaining a lot of commands and will attempt to finish the individual assignment by the end of tonight.

''— [[User:Rlegaspi|Rlegaspi]] ([[User talk:Rlegaspi|talk]]) 17:19, 20 September 2015 (PDT)

----

== Week 1 Feedback ==

* I answered your question on my [[User_talk:Kdahlquist | User talk page.]]
* The scores have not been posted yet, but I wanted to give you feedback on your [[Week 1]] Assignment.
* Your individual assignment was late (submitted at 03:01), your questions on our talk pages were late (submitted at 02:38 and 02:42), and your shared assignment was late (submitted at 02:45). In the future, make sure to give yourself enough time to complete the assignment so that you do not submit your work late.
* Your assignment is complete except for the items that I list below. I particularly like how you took advantage of external links in your work history and other areas of your page. Your work history could be improved by making further sub-bullets after you give the location and dates of your employment. You wrote something in the Summary field 100% of the time, good work!
* Missing items:
*# You did not send an e-mail to myself and Dr. Dionisio answering the questions whether you had any concerns or whether there was anything else you wanted us to know. Please e-mail us with your answers, even if your answers are "no".
*# You need to upload an image and use it on your page.
*# You need to upload another type of file and link to it on your page.
* You will have the opportunity to make up some of the points you missed by completing the tasks listed above by the [[Week 2]] deadline, midnight on September 15.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:43, 8 September 2015 (PDT)''

== Week 1 Feedback Response ==

* Thank you for answering the question.
* I apologize for the late submissions. I didn't expect to work so much over the Labor Day Weekend and was only able to finish my page after the closing shift. I will upload an image of myself and a few images relating to the content on my page; in addition to another type of file.
* Again, I appreciate the feedback. I am going to do a better job of spreading out my tasks and staying true to my weekly study plan.

''— [[User:Rlegaspi|Rlegaspi]] ([[User talk:Rlegaspi|talk]]) 13:59, 8 September 2015 (PDT)

----

I’ve answered your question on my [[User_talk:Dondi | talk page]].

''—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:56, 12 September 2015 (PDT)''

Gene Database Testing Report - Heavy Metal HaterZ

2015-12-03T23:55:55Z

Kdahlquist: /* Analysis */ note on extra IDs

{{Heavy Metal HaterZ}}
==Export Information==

Version of GenMAPP Builder: '''3 build 5'''

Computer on which export was run: '''HP Compaq 8300 Elite SFF FC'''

Postgres Database name: '''S. Oneidensis'''

UniProt XML filename: [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']]
* UniProt XML version: '''UniProt release 2015_10 - October 14, 2015'''
* [http://www.uniprot.org/uniprot/?query=taxonomy:211586 UniProt XML download link]
* Time taken to import: '''3.18 minutes'''
** Note: ''n/a''

GO OBO-XML filename: [[Media:Go daily-termdb.obo-xml.gz | '''go daily-termdb.obo-xml''']]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* [http://geneontology.org/page/download-ontology#Legacy_Downloads GO OBO-XML download link]
* Time taken to import: '''7.16 minutes'''
* Time taken to process: '''4.27 minutes'''
** Note: ''n/a''

GOA filename: [[Media:ShewanellaOneidensisGOA.zip | '''ShewanellaOneidensisGOA''']]
* 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]): '''October 14, 2015 - GOA Proteome Sets 124'''
* [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/106.S_oneidensis.goa GOA download link]
* Time taken to import: '''0.05 minutes'''
** Note: ''n/a''

Name of .gdb file: [[Media:So-Std 20151119HMH.zip | '''So-Std 20151119HMH.gdb''']]
* Time taken to export: '''1 hour and 18 minutes'''
** Start time: '''3:48pm'''
** End time: '''5:06pm'''
** Note: ''n/a''

==TallyEngine==

* Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the Postgres databases.
** Choose the menu item Tallies > Run XML and Database Tallies for UniProt and GO...
** Take a screenshot of the results. Upload the image to the wiki and display it on this page.
** '''4196''' IDs
** For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

[[Image:TallyEngineSOneidensis.PNG | center | 540px]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | 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?
* Initially, we got '''4196''' IDs for both XML and Postgres DB from TallyEngine but got '''4079''' IDs by using XMLPipeDB match. This result was from using the following command:
java -jar xmlpipedb-match-1.1.1.jar "SO_[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT

* After checking the .gdb file and looking through the Gene IDs, I found that some IDs were in the form "SO_A####" so I ran a new command accounting for this:
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* This gave a total number of '''4207''' IDs.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

You can also look for counts at the SQL level, using some variation of a ''select count(*)'' query. This requires some knowledge of which table received what data. Here’s an initial tip: the ''gene/name'' tags in the XML file land in the ''genenametype'' table. A query on this table counting values from this table that were marked as ''ordered locus'' in the XML file matching the pattern ''SO_[0-9][0-9][0-9][0-9]'' would look like this:

select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_[0-9][0-9][0-9][0-9]';
* However, once I found that some IDs were in the form "SO_A####" I tweaked the pattern to account for those IDs:
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';

In ''pgAdmin III'', you can issue these queries by clicking on the pencil/SQL icon in the toolbar, typing the query into the ''SQL Editor'' tab, then clicking on the green triangular ''Play'' button to run.

Are your results the same as reported by the TallyEngine? Why or why not?
* Initially, we got a count of '''4068''' IDs using SQL, which differed from the '''4196''' IDs from TallyEngine.
* After tweaking the pattern to account for IDs with that extra ''A'', we got a grand total of '''4196''' IDs, which matches with what TallyEngine gave us.

==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: [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download 2010 benchmark file]

Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:

[[Media:OriginalRowCounts.pdf | Original Row Counts Table]]

[[Media:OriginalRowCounts2010.pdf | 2010 Benchmark Original Row Counts Table]]

See Analysis section for more on the comparison and the discrepancy found because of this comparison.

Note: Using Microsoft Access, we found ''7664'' IDs, which was actually double the number of IDs present because of duplicated IDs that did not have an underscore.

==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?
** No. For the current version, a good number of gene ID systems in the database do not have a value for the date field. Some systems that lack a date include: GenBank, UniGene, WormBase, and EcoGene.
* 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?
** For the UniProt table, the IDs start with either ''Q8'' or ''K4'' and have some string of four letters/numbers trailing that. For the RefSeq tables, the IDs have forms that start with either ''NP_'' or ''WP_'', with the ''WP_'' forms having 9 numbers afterwards and the ''NP_'' forms having 6 numbers afterwards. For the OrderedLocusNames table, the IDs either start with <code>SO_</code> or <code>SO_A</code>.

Note: ''n/a''

==Analysis==

Consolidating the counts of gene IDs from the various methods, I got:

* 4196 IDs from Tally Engine
* ''4207'' IDs from xmlpipedb-match
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* 4196 IDs from PostgreSQL
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';
* 4196 IDs from Microsoft Access (Noted that there were 4068 IDs in the form <code>SO_####</code> and 128 IDs in the form <code>SO_A####</code>)

Notice that there is a small but significant discrepancy in that there seems to be eleven more IDs when using xmlpipedb-match. This is troubling because of the fact that the other three methods seemed to confirm a total count of 4196. So, I used Microsoft Excel to compare the list of gene IDs from the actual .gdb file and the list I got back from xmlpipedb-match. As you can see on [[Media:Comparing gdb and xmlpipedb-match.xlsx | this document]], there are 11 IDs in the xmlpipedb-match column that are not found in the gdb column. This discrepancy was further pointed out by the use of some <code>match</code> functions to see where an ID was missing from either list. Below are the two match functions I used in the document:
=MATCH(A2, B$2:B$4208, 0)
=MATCH(B2, A$2:A$4208, 0)
Below are the eleven IDs in question:
SO_3699 NO-KD
SO_1312 NO-KD
SO_4269 NO-KD if they are all part of "Protein-protein interaction databases", then you can safely leave them out
SO_2875
SO_4532
SO_4580
SO_2662
SO_4423
SO_3156
SO_2967
SO_2024

Look up the IDs at [http://www.uniprot.org UniProt web site] and then search for them on the UniProt record web page. If they are part of the "STRING" protein-protein interaction database, then you can safely leave them out. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 3 December 2015 (PST)''

None of these IDs are in our MOD.
We searched for these IDs in the microarray statistical analysis sheet and did not find the following IDs:
SO_4269, SO_2875, SO_4580

As of 12/01/15, we are waiting on input from Professor Dahlquist to see if we will adjust our GenMAPP Builder to account for these 11 IDs.
* A manual inspection was done on the [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']] XML file and it looks like these 11 IDs are contained within entries that are missing a gene tag, which explains why the other methods only picked up 4196 IDs.

==.gdb Use in GenMAPP==

While the above sections perform quality assurance on the exported Gene Database via verifying ID counts, the "proof in the pudding" is to actually use the Gene Database in GenMAPP. You can follow the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] to verify that the Gene Database works in GenMAPP. In this case, the emphasis is not on the findings of the data analysis itself, but that the Gene Database functions appropriate in GenMAPP.

For assistance with using the GenMAPP program, the GenMAPP Help is very extensive. To access it within GenMAPP, go to the menu item Help > GenMAPP Help and either browse or search for your topic of interest.

Note: ''n/a''

===Putting a gene on the MAPP using the GeneFinder window===

* In the main GenMAPP Drafting Board window, left-click on the icon for "Gene" in the upper left corner of the window. Click on the Drafting Board to place the Gene on the MAPP. Now, right-click on the gene to access the GeneFinder window. Type or paste a gene ID into the Gene ID field. Select the appropriate Gene ID system from the drop-down menu and click the Search button. For example, for ''Vibrio cholerae'', you could search for the ID "VC0028", which is an OrderedLocusNames ID. Once the ID has been found, click the OK button to return to the Drafting Board window.
** For the Final Project, you will need to try a sample ID from each of the gene ID systems, not just OrderedLocusNames.
* Open the Backpage by left-clicking on the gene box on the Drafting Board to see if all of the cross-referenced IDs that are supposed to be there are there.

Note: I tried out the search for a gene ID and was able to bring up the Backpage for that ID. The cross-referenced IDs that were supposed to show up were indeed on the page.

===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: The Expression Dataset Manager reported that there were 121 errors during the conversion. From looking over the error codes, I found that all errors were of the form: <code>Gene not found in OrderedLocusNames or any related system.</code> It seems that these IDs were in fact not present in the UniProt XML.

===Coloring a MAPP with expression data===

Note: I was able to successfully color the MAPP by coloring the increased and decreased Log Fold Changes.

===Running MAPPFinder===

Note: After the results had been calculated, a Gene Ontology browser opened showing my results. All of the Gene Ontology terms that have at least 3 genes measured and a p value of less than 0.05 were highlighted yellow. A term with a p value less than 0.05 is considered a "significant" result. Browsed through the tree to see the results.

Documents produced from this run-through can be found here: [[Media:Week 9 genMAPP and MAPPFinder.zip | week 9 docs]]

Gene Database Testing Report - Heavy Metal HaterZ

2015-12-03T23:51:28Z

Kdahlquist: /* Analysis */ result for second ID

{{Heavy Metal HaterZ}}
==Export Information==

Version of GenMAPP Builder: '''3 build 5'''

Computer on which export was run: '''HP Compaq 8300 Elite SFF FC'''

Postgres Database name: '''S. Oneidensis'''

UniProt XML filename: [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']]
* UniProt XML version: '''UniProt release 2015_10 - October 14, 2015'''
* [http://www.uniprot.org/uniprot/?query=taxonomy:211586 UniProt XML download link]
* Time taken to import: '''3.18 minutes'''
** Note: ''n/a''

GO OBO-XML filename: [[Media:Go daily-termdb.obo-xml.gz | '''go daily-termdb.obo-xml''']]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* [http://geneontology.org/page/download-ontology#Legacy_Downloads GO OBO-XML download link]
* Time taken to import: '''7.16 minutes'''
* Time taken to process: '''4.27 minutes'''
** Note: ''n/a''

GOA filename: [[Media:ShewanellaOneidensisGOA.zip | '''ShewanellaOneidensisGOA''']]
* 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]): '''October 14, 2015 - GOA Proteome Sets 124'''
* [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/106.S_oneidensis.goa GOA download link]
* Time taken to import: '''0.05 minutes'''
** Note: ''n/a''

Name of .gdb file: [[Media:So-Std 20151119HMH.zip | '''So-Std 20151119HMH.gdb''']]
* Time taken to export: '''1 hour and 18 minutes'''
** Start time: '''3:48pm'''
** End time: '''5:06pm'''
** Note: ''n/a''

==TallyEngine==

* Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the Postgres databases.
** Choose the menu item Tallies > Run XML and Database Tallies for UniProt and GO...
** Take a screenshot of the results. Upload the image to the wiki and display it on this page.
** '''4196''' IDs
** For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

[[Image:TallyEngineSOneidensis.PNG | center | 540px]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | 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?
* Initially, we got '''4196''' IDs for both XML and Postgres DB from TallyEngine but got '''4079''' IDs by using XMLPipeDB match. This result was from using the following command:
java -jar xmlpipedb-match-1.1.1.jar "SO_[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT

* After checking the .gdb file and looking through the Gene IDs, I found that some IDs were in the form "SO_A####" so I ran a new command accounting for this:
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* This gave a total number of '''4207''' IDs.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

You can also look for counts at the SQL level, using some variation of a ''select count(*)'' query. This requires some knowledge of which table received what data. Here’s an initial tip: the ''gene/name'' tags in the XML file land in the ''genenametype'' table. A query on this table counting values from this table that were marked as ''ordered locus'' in the XML file matching the pattern ''SO_[0-9][0-9][0-9][0-9]'' would look like this:

select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_[0-9][0-9][0-9][0-9]';
* However, once I found that some IDs were in the form "SO_A####" I tweaked the pattern to account for those IDs:
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';

In ''pgAdmin III'', you can issue these queries by clicking on the pencil/SQL icon in the toolbar, typing the query into the ''SQL Editor'' tab, then clicking on the green triangular ''Play'' button to run.

Are your results the same as reported by the TallyEngine? Why or why not?
* Initially, we got a count of '''4068''' IDs using SQL, which differed from the '''4196''' IDs from TallyEngine.
* After tweaking the pattern to account for IDs with that extra ''A'', we got a grand total of '''4196''' IDs, which matches with what TallyEngine gave us.

==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: [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download 2010 benchmark file]

Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:

[[Media:OriginalRowCounts.pdf | Original Row Counts Table]]

[[Media:OriginalRowCounts2010.pdf | 2010 Benchmark Original Row Counts Table]]

See Analysis section for more on the comparison and the discrepancy found because of this comparison.

Note: Using Microsoft Access, we found ''7664'' IDs, which was actually double the number of IDs present because of duplicated IDs that did not have an underscore.

==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?
** No. For the current version, a good number of gene ID systems in the database do not have a value for the date field. Some systems that lack a date include: GenBank, UniGene, WormBase, and EcoGene.
* 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?
** For the UniProt table, the IDs start with either ''Q8'' or ''K4'' and have some string of four letters/numbers trailing that. For the RefSeq tables, the IDs have forms that start with either ''NP_'' or ''WP_'', with the ''WP_'' forms having 9 numbers afterwards and the ''NP_'' forms having 6 numbers afterwards. For the OrderedLocusNames table, the IDs either start with <code>SO_</code> or <code>SO_A</code>.

Note: ''n/a''

==Analysis==

Consolidating the counts of gene IDs from the various methods, I got:

* 4196 IDs from Tally Engine
* ''4207'' IDs from xmlpipedb-match
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* 4196 IDs from PostgreSQL
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';
* 4196 IDs from Microsoft Access (Noted that there were 4068 IDs in the form <code>SO_####</code> and 128 IDs in the form <code>SO_A####</code>)

Notice that there is a small but significant discrepancy in that there seems to be eleven more IDs when using xmlpipedb-match. This is troubling because of the fact that the other three methods seemed to confirm a total count of 4196. So, I used Microsoft Excel to compare the list of gene IDs from the actual .gdb file and the list I got back from xmlpipedb-match. As you can see on [[Media:Comparing gdb and xmlpipedb-match.xlsx | this document]], there are 11 IDs in the xmlpipedb-match column that are not found in the gdb column. This discrepancy was further pointed out by the use of some <code>match</code> functions to see where an ID was missing from either list. Below are the two match functions I used in the document:
=MATCH(A2, B$2:B$4208, 0)
=MATCH(B2, A$2:A$4208, 0)
Below are the eleven IDs in question:
SO_3699 NO-KD
SO_1312 NO-KD
SO_4269
SO_2875
SO_4532
SO_4580
SO_2662
SO_4423
SO_3156
SO_2967
SO_2024

None of these IDs are in our MOD.
We searched for these IDs in the microarray statistical analysis sheet and did not find the following IDs:
SO_4269, SO_2875, SO_4580

As of 12/01/15, we are waiting on input from Professor Dahlquist to see if we will adjust our GenMAPP Builder to account for these 11 IDs.
* A manual inspection was done on the [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']] XML file and it looks like these 11 IDs are contained within entries that are missing a gene tag, which explains why the other methods only picked up 4196 IDs.

==.gdb Use in GenMAPP==

While the above sections perform quality assurance on the exported Gene Database via verifying ID counts, the "proof in the pudding" is to actually use the Gene Database in GenMAPP. You can follow the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] to verify that the Gene Database works in GenMAPP. In this case, the emphasis is not on the findings of the data analysis itself, but that the Gene Database functions appropriate in GenMAPP.

For assistance with using the GenMAPP program, the GenMAPP Help is very extensive. To access it within GenMAPP, go to the menu item Help > GenMAPP Help and either browse or search for your topic of interest.

Note: ''n/a''

===Putting a gene on the MAPP using the GeneFinder window===

* In the main GenMAPP Drafting Board window, left-click on the icon for "Gene" in the upper left corner of the window. Click on the Drafting Board to place the Gene on the MAPP. Now, right-click on the gene to access the GeneFinder window. Type or paste a gene ID into the Gene ID field. Select the appropriate Gene ID system from the drop-down menu and click the Search button. For example, for ''Vibrio cholerae'', you could search for the ID "VC0028", which is an OrderedLocusNames ID. Once the ID has been found, click the OK button to return to the Drafting Board window.
** For the Final Project, you will need to try a sample ID from each of the gene ID systems, not just OrderedLocusNames.
* Open the Backpage by left-clicking on the gene box on the Drafting Board to see if all of the cross-referenced IDs that are supposed to be there are there.

Note: I tried out the search for a gene ID and was able to bring up the Backpage for that ID. The cross-referenced IDs that were supposed to show up were indeed on the page.

===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: The Expression Dataset Manager reported that there were 121 errors during the conversion. From looking over the error codes, I found that all errors were of the form: <code>Gene not found in OrderedLocusNames or any related system.</code> It seems that these IDs were in fact not present in the UniProt XML.

===Coloring a MAPP with expression data===

Note: I was able to successfully color the MAPP by coloring the increased and decreased Log Fold Changes.

===Running MAPPFinder===

Note: After the results had been calculated, a Gene Ontology browser opened showing my results. All of the Gene Ontology terms that have at least 3 genes measured and a p value of less than 0.05 were highlighted yellow. A term with a p value less than 0.05 is considered a "significant" result. Browsed through the tree to see the results.

Documents produced from this run-through can be found here: [[Media:Week 9 genMAPP and MAPPFinder.zip | week 9 docs]]

Gene Database Testing Report - Heavy Metal HaterZ

2015-12-03T23:48:11Z

Kdahlquist: /* Analysis */ putting a no if should not include

{{Heavy Metal HaterZ}}
==Export Information==

Version of GenMAPP Builder: '''3 build 5'''

Computer on which export was run: '''HP Compaq 8300 Elite SFF FC'''

Postgres Database name: '''S. Oneidensis'''

UniProt XML filename: [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']]
* UniProt XML version: '''UniProt release 2015_10 - October 14, 2015'''
* [http://www.uniprot.org/uniprot/?query=taxonomy:211586 UniProt XML download link]
* Time taken to import: '''3.18 minutes'''
** Note: ''n/a''

GO OBO-XML filename: [[Media:Go daily-termdb.obo-xml.gz | '''go daily-termdb.obo-xml''']]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* [http://geneontology.org/page/download-ontology#Legacy_Downloads GO OBO-XML download link]
* Time taken to import: '''7.16 minutes'''
* Time taken to process: '''4.27 minutes'''
** Note: ''n/a''

GOA filename: [[Media:ShewanellaOneidensisGOA.zip | '''ShewanellaOneidensisGOA''']]
* 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]): '''October 14, 2015 - GOA Proteome Sets 124'''
* [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/106.S_oneidensis.goa GOA download link]
* Time taken to import: '''0.05 minutes'''
** Note: ''n/a''

Name of .gdb file: [[Media:So-Std 20151119HMH.zip | '''So-Std 20151119HMH.gdb''']]
* Time taken to export: '''1 hour and 18 minutes'''
** Start time: '''3:48pm'''
** End time: '''5:06pm'''
** Note: ''n/a''

==TallyEngine==

* Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the Postgres databases.
** Choose the menu item Tallies > Run XML and Database Tallies for UniProt and GO...
** Take a screenshot of the results. Upload the image to the wiki and display it on this page.
** '''4196''' IDs
** For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

[[Image:TallyEngineSOneidensis.PNG | center | 540px]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | 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?
* Initially, we got '''4196''' IDs for both XML and Postgres DB from TallyEngine but got '''4079''' IDs by using XMLPipeDB match. This result was from using the following command:
java -jar xmlpipedb-match-1.1.1.jar "SO_[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT

* After checking the .gdb file and looking through the Gene IDs, I found that some IDs were in the form "SO_A####" so I ran a new command accounting for this:
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* This gave a total number of '''4207''' IDs.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

You can also look for counts at the SQL level, using some variation of a ''select count(*)'' query. This requires some knowledge of which table received what data. Here’s an initial tip: the ''gene/name'' tags in the XML file land in the ''genenametype'' table. A query on this table counting values from this table that were marked as ''ordered locus'' in the XML file matching the pattern ''SO_[0-9][0-9][0-9][0-9]'' would look like this:

select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_[0-9][0-9][0-9][0-9]';
* However, once I found that some IDs were in the form "SO_A####" I tweaked the pattern to account for those IDs:
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';

In ''pgAdmin III'', you can issue these queries by clicking on the pencil/SQL icon in the toolbar, typing the query into the ''SQL Editor'' tab, then clicking on the green triangular ''Play'' button to run.

Are your results the same as reported by the TallyEngine? Why or why not?
* Initially, we got a count of '''4068''' IDs using SQL, which differed from the '''4196''' IDs from TallyEngine.
* After tweaking the pattern to account for IDs with that extra ''A'', we got a grand total of '''4196''' IDs, which matches with what TallyEngine gave us.

==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: [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download 2010 benchmark file]

Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:

[[Media:OriginalRowCounts.pdf | Original Row Counts Table]]

[[Media:OriginalRowCounts2010.pdf | 2010 Benchmark Original Row Counts Table]]

See Analysis section for more on the comparison and the discrepancy found because of this comparison.

Note: Using Microsoft Access, we found ''7664'' IDs, which was actually double the number of IDs present because of duplicated IDs that did not have an underscore.

==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?
** No. For the current version, a good number of gene ID systems in the database do not have a value for the date field. Some systems that lack a date include: GenBank, UniGene, WormBase, and EcoGene.
* 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?
** For the UniProt table, the IDs start with either ''Q8'' or ''K4'' and have some string of four letters/numbers trailing that. For the RefSeq tables, the IDs have forms that start with either ''NP_'' or ''WP_'', with the ''WP_'' forms having 9 numbers afterwards and the ''NP_'' forms having 6 numbers afterwards. For the OrderedLocusNames table, the IDs either start with <code>SO_</code> or <code>SO_A</code>.

Note: ''n/a''

==Analysis==

Consolidating the counts of gene IDs from the various methods, I got:

* 4196 IDs from Tally Engine
* ''4207'' IDs from xmlpipedb-match
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* 4196 IDs from PostgreSQL
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';
* 4196 IDs from Microsoft Access (Noted that there were 4068 IDs in the form <code>SO_####</code> and 128 IDs in the form <code>SO_A####</code>)

Notice that there is a small but significant discrepancy in that there seems to be eleven more IDs when using xmlpipedb-match. This is troubling because of the fact that the other three methods seemed to confirm a total count of 4196. So, I used Microsoft Excel to compare the list of gene IDs from the actual .gdb file and the list I got back from xmlpipedb-match. As you can see on [[Media:Comparing gdb and xmlpipedb-match.xlsx | this document]], there are 11 IDs in the xmlpipedb-match column that are not found in the gdb column. This discrepancy was further pointed out by the use of some <code>match</code> functions to see where an ID was missing from either list. Below are the two match functions I used in the document:
=MATCH(A2, B$2:B$4208, 0)
=MATCH(B2, A$2:A$4208, 0)
Below are the eleven IDs in question:
SO_3699 NO-KD
SO_1312
SO_4269
SO_2875
SO_4532
SO_4580
SO_2662
SO_4423
SO_3156
SO_2967
SO_2024

None of these IDs are in our MOD.
We searched for these IDs in the microarray statistical analysis sheet and did not find the following IDs:
SO_4269, SO_2875, SO_4580

As of 12/01/15, we are waiting on input from Professor Dahlquist to see if we will adjust our GenMAPP Builder to account for these 11 IDs.
* A manual inspection was done on the [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']] XML file and it looks like these 11 IDs are contained within entries that are missing a gene tag, which explains why the other methods only picked up 4196 IDs.

==.gdb Use in GenMAPP==

While the above sections perform quality assurance on the exported Gene Database via verifying ID counts, the "proof in the pudding" is to actually use the Gene Database in GenMAPP. You can follow the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] to verify that the Gene Database works in GenMAPP. In this case, the emphasis is not on the findings of the data analysis itself, but that the Gene Database functions appropriate in GenMAPP.

For assistance with using the GenMAPP program, the GenMAPP Help is very extensive. To access it within GenMAPP, go to the menu item Help > GenMAPP Help and either browse or search for your topic of interest.

Note: ''n/a''

===Putting a gene on the MAPP using the GeneFinder window===

* In the main GenMAPP Drafting Board window, left-click on the icon for "Gene" in the upper left corner of the window. Click on the Drafting Board to place the Gene on the MAPP. Now, right-click on the gene to access the GeneFinder window. Type or paste a gene ID into the Gene ID field. Select the appropriate Gene ID system from the drop-down menu and click the Search button. For example, for ''Vibrio cholerae'', you could search for the ID "VC0028", which is an OrderedLocusNames ID. Once the ID has been found, click the OK button to return to the Drafting Board window.
** For the Final Project, you will need to try a sample ID from each of the gene ID systems, not just OrderedLocusNames.
* Open the Backpage by left-clicking on the gene box on the Drafting Board to see if all of the cross-referenced IDs that are supposed to be there are there.

Note: I tried out the search for a gene ID and was able to bring up the Backpage for that ID. The cross-referenced IDs that were supposed to show up were indeed on the page.

===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: The Expression Dataset Manager reported that there were 121 errors during the conversion. From looking over the error codes, I found that all errors were of the form: <code>Gene not found in OrderedLocusNames or any related system.</code> It seems that these IDs were in fact not present in the UniProt XML.

===Coloring a MAPP with expression data===

Note: I was able to successfully color the MAPP by coloring the increased and decreased Log Fold Changes.

===Running MAPPFinder===

Note: After the results had been calculated, a Gene Ontology browser opened showing my results. All of the Gene Ontology terms that have at least 3 genes measured and a p value of less than 0.05 were highlighted yellow. A term with a p value less than 0.05 is considered a "significant" result. Browsed through the tree to see the results.

Documents produced from this run-through can be found here: [[Media:Week 9 genMAPP and MAPPFinder.zip | week 9 docs]]

File:Bpertussis CompiledRawData MS2015.xlsx

2015-12-03T23:42:36Z

Kdahlquist: Kdahlquist uploaded a new version of File:Bpertussis CompiledRawData MS2015.xlsx

File:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx

2015-12-03T23:02:09Z

Kdahlquist: Kdahlquist uploaded a new version of File:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx

KZ Compiled Raw Data file from 1/21 through Scaling/Centering. I focused on RX and Erich did RP.

File:CompiledRawData 20151201 HMH.xlsx

2015-12-02T18:21:54Z

Kdahlquist: Kdahlquist uploaded a new version of File:CompiledRawData 20151201 HMH.xlsx

User talk:Lenaolufson

2015-12-02T00:38:58Z

Kdahlquist: instructions on how to fix workbook

[[Elena Olufson]]

----

[[Template:Lenaolufson]]

== "100000" issue ==

* Lena, I've looked at the file. While I was looking, I uncovered an issue with how you made your "MasterSheet" worksheet. You were only supposed to copy over the columns that had the correct Cy5/Cy3 orientation. There should only be two technical replicates per sample in your MasterSheet.
* First fix your MasterSheet by getting rid of the columns you don't need.
* What we will do next is not delete the genes, but do a search and replace. You will search for "100000" and "-1000000" and replace it with an empty cell. In the find/replace window, type 100000 or -100000 in the find field and nothing at all in the replace field and then click on the replace all button and record the number of replacements.
* Then you can copy and paste special > paste values into your scaling and centering sheet and try again. You will know things are OK if your Average for each column is a very small number near zero and your standard deviation is near 1.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:38, 1 December 2015 (PST)''

== Week 12 Feedback ==

* I've looked at the compiled raw data that you posted and I have some feedback and next steps.
*# Rename Sheet1 to "CompiledRawData".
*# Rename your column heading as follows:
*#* Call your leftmost column "ID" instead of Code.
*#* For the data columns, you can get rid of the "(635/532)" from each header. While I understand what you are doing with the "A3-A5" nomenclature, it would be a little more clear if you called it something like "LogRatio_SampleA_Cy3-Cy5".
*# Once you have renamed the columns, do all further manipulations in a different sheet. Copy and paste all of the data into Sheet2 which you should rename to "DyeSwap".
*# Create a "MasterIndex" column as follows. Insert a new column to the right of the "ID" column and name it "MasterIndex". In this column you will create a numerical index of genes so that you can always sort them back into the same order that they started out in.
*#* Type a "1" in cell B2 and a "2" in cell B3.
*#* Select both cells. Hover your mouse over the bottom-right corner of the selection until it makes a thin black + sign. Double-click on the + sign to fill the entire column with a series of numbers from 1 to 8448 (the number of spots on the microarray).
*# Now, select all of the data and sort it A-->Z on the "ID" column.
*# Delete all of the rows that have an ID of "_". Record the number of records left after you do that.
*# Now you need to swap the dye orientation so that all of the samples are Cy5/Cy3.
*#* Insert a column to the right of the columns that need to be swapped. Name the new column the same as you did before, but addd "_swapped" to the header to designate that you are going to swap the samples.
*#* Then, type a formula in the column where you multiply the value that needs to be swapped by (-1). Copy and paste the formula to the entire column.
*# Create a new worksheet that you name "MasterSheet". Copy and Paste special > Paste values the ID, MasterIndex, and data columns that are all in the orientation of Cy5/Cy3 (the original ones and the ones you just swapped).
*# This is now your the starting point for the normalization and statistics. Copy and paste the data from this sheet into a new worksheet, which you should rename "ScalingCentering".
*# In this new sheet, you should perform the scaling and centering according to the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae ''Vibrio cholerae'' instructions found here.]]
*# At this point, post your spreadsheet and e-mail Dr. Dahlquist and let me know where to find it. Your particular chip has duplicated spots on it, which we should average as another type of technical replicate. I have a script that will separate out the IDs so that you can easily average them in Excel. I will run the script and give you the results before you move on.
*# Once this has been done, you will create a new sheet called "Statistics" and paste the values into this sheet.
*#* You will then compute the average of the duplicate spots on the chip to get one value per chip.
*#* You will then compute the average of the dye-swapped technical replicates to get one value per sample (A, B, C).
*#* You will then compute the average of the averages for A, B, and C, to get the average of all samples.
*#* You can then you should compute the T statistic, P value, Bonferroni adjusted p value, and Benjamini and Hochberg adjusted p value, according to the instructions you used for ''Vibrio cholerae.''
*# After that, then you will need to then format it for GenMAPP and you'll be ready to import it into GenMAPP and run MAPPFinder.
* Let me know if have questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:16, 24 November 2015 (PST)''

== Week 6 Feedback ==

I’ve chosen to issue partial feedback sooner than complete feedback later, in case it will help you address issues with [[Week 8]].

=== Best Practices ===

* Individual and shared work were both submitted on time.
* Almost all requisite links to and from the user page as well as page categories are present, except:
** The link from the individual journal entry back to your user page was missed.
* Electronic notebook was maintained.
* Work was submitted with corresponding summaries, but there were only 5 submissions. An assignment of this size can definitely be completed in smaller milestones; it is ideal to save your work after each of these milestones.

=== Database Exercises ===

Work in progress.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:24, 25 October 2015 (PDT)''

== Week 4 Feedback ==

* Work was submitted mostly on time, with a small fix applied the next day.
* All good-habit items are largely fulfilled, with some suggestions for improvement:
** All expected links and categories were noted, but the link from the journal entry to the user page is not part of the template. It will save you future trouble of you integrate this.
** Electronic notebook content was seen.
** Summaries were consistently provided for all edits, although there were only 5 of them. An assignment of this scale could certainly have been broken up into smaller pieces; this ensures that less work will be lost in the event of a power, software, or network failure.
* For the exercises, the following issues were seen; all others were correct:
** You were off by one nucleotide on the transcription start site.
** Because the transcription start site was off by one nucleotide, then the mRNA sequence was off by that single base as well.
* Shared responses were provided and they came in on time.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 12:46, 7 October 2015 (PDT)''

== Week 3 Full Feedback ==

In addition to the early “good habit” notes previously given below, the following notes complete my response to your submissions:
* All of your command-line answers showed the correct results. Good job!
* One suggestion for presenting either code or plain data: if you begin a wiki line with an empty space, the text that follows it will be format in a “fixed width” format that fits code or plain data better. Give it a try and see how it looks to you.
* Regarding your shared journal entry, practice is definitely the way to get more comfortable with the command line. Allow yourself to make mistakes—with the commands that I have shown you so far, mistakes will be harmless and you can learn from them. There is definitely an unprecedented level of detail and precision involved when working with computers in this manner; but, as your chosen quote says, there is ultimately an art to it. Many arts require the same level of precision—you can think of coding precision as a very similar kind of exactitude.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 16:52, 26 September 2015 (PDT)''

== Week 3 Early Feedback ==

My week 3 grading is not finished, but based on your week 2 feedback and what I have seen so far in Week 3, I thought I would chime in early so you can try to address these by the week 4 assignment.
* Good job in supplying a summary with all of your wiki contributions in Week 3! This is a good habit to maintain throughout the semester. You also accomplished this with a few more edits, which is also something to reinforce.
* Your Week 3 assignment still did not use the template that you’ve created; do make sure that you do so in Week 4 and beyond, because it contains all of the useful links that are checked for every assignment.
** Please see Dr. Dahlquist’s instructions above for using the template in your journal pages.
** Also make sure to add a link to your User Page within the template.
* Week 3 does not include the ''Journal Entry'' category either.
* Finally, a lab notebook aspect continues to be missing from your Week 3 submission. Your responses are almost entirely just the answers, with no notes on your thought process. As the computing assignments get harder, you will find this to be more and more crucial. Please give it a shot for Week 4.
That’s not everything yet, but I figured these were good points to make so that you can get a jump on them for Week 4.

—''[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:18, 24 September 2015 (PDT)''

== Week 2 Feedback ==

* Although, the [[Week 2]] scores have not yet been posted, I want to give you feedback on the assignment that you can incorporate to your your [[Week 3]] submission.
* First, thank you for submitting your assignment on time.
* Your translations are correct; although it would have been better for completeness to go ahead and translate the rest of the sequence after the stop codon, in this case.
* You did not include anything by the way of an electronic notebook for this assignment. Although this assignment was pretty straightforward, you still need to document the process of what you did to arrive at the answers, not just supply the answers. Please be sure to do this for your Week 3 submission.
* You wrote something in the Summary field for 7/14 contributions between the Week 1 and Week 2 deadlines. We are aiming to do this 100% of the time, so this needs a little work. Also, you completed the full assignment in only 3 edits to the wiki. You will want to consider saving your changes more frequently so that the granularity of the changes is smaller.
* For each week's assignment, you will need to create links from your User page to that week's assignment and to your individual and shared journal entries, as well as a link back from your individual journal entry and to the category "Journal Entry".
** You have actually created all of these links on your template page (by borrowing the formatting from a fellow student, I see). However, what is missing is that you need to actually '''''invoke''''' the template on your user page and individual journal entry pages.
*** To do so, you need to use the syntax <nowiki>{{Lenaolufson}}</nowiki>, with the curly brackets, on your user page and on your [[Lenaolufson Week 2]] page.
*** You could even invoke your template on all of your future individual journal assignment pages now, so you would never forget to do it again and would also avoid losing points for not providing the links.
* If you begin a line with a single space character, the text will appear in a fixed-width font, which is better for representing nucleic acid and protein sequences because they will then line up with each other better.
* With regards to your comments on your shared journal entry, you will see from the other students' comments, that others had issues with the Kaji and Kaji paper. It is sometimes the shortest papers that are the most difficult to understand!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:32, 18 September 2015 (PDT)''

== Week 1 Feedback ==

* I answered your question on my [[User_talk:Dondi|User talk page]].
* The scores have not been posted yet, but I wanted to give you feedback on your [[Week 1]] Assignment.
* Except for the email to Dr. Dahlquist and me, your assignment was submitted on time overall. Many of our assignments will be multipart like this one, so getting into a checklist habit will help you cover all the bases.
* Speaking of a checklist approach, your assignment is complete except for the items that I list below. I particularly like how you took advantage of external links in your work history and other areas of your page. You wrote something in the Summary field most of the time, although some were just generic indications of what sections got changed. See if you can get more descriptive as you get the hang of this; you’ll find that it makes your work more deliberate.
* Missing items:
*# You did not indicate a snail mail address; withholding it on purpose is fine (say, for privacy reasons due to an off-campus address), but just as with the email to Dr. Dahlquist and me, we would have preferred an indication to that effect, to differentiate between forgetting to do it vs. not forgetting but preferring not to supply it.
*# You defined headings down to just one level. Try to do multiple levels, at least 3 when appropriate, so that you can see how the headings give your page an outline structure.
*# You created numbered lists as instructed, although in the Personal Interests section, with those single-item lists, a bulleted format would have been more appropriate. Even though you are checking off subtasks in this assignment, ideally you are also performing them in a context that matches their purpose well.
*# Similarly, you did technically create and use a template, but said template does not really hold content that benefits from template automation. Ideally, your template contains something that will genuinely save you a lot of retyping in the future. The example that we mentioned in class was a template holding a quick-reference list for all of your pages—that will be ''very'' useful as a template because you will want to include that in every page you create, and will be a pain to retype every time. So, consider those practical elements when choosing to practice the basic wiki skills. That way it isn’t just a rote exercise and is actually something is useful for the rest of the semester.
* You will have the opportunity to make up some of the points you missed by completing the tasks listed above by the [[Week 2]] deadline, midnight on September 15.

''—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:14, 9 September 2015 (PDT)''

I have also answered your question on my [[User_talk:Kdahlquist | user talk page.]] ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:18, 10 September 2015 (PDT)''

Gene Database Project

2015-12-01T23:42:17Z

Kdahlquist: /* Group Deliverables */ added link to Markdown version of readme

{{Gene Database Project Links}}

== Deliverables ==

* You will give a final group [[Gene_Database_Project_Deliverables#PowerPoint_Presentation | PowerPoint presentation]] in class during the final exam period on '''Tuesday, December 15, 2:00pm'''.
* Final due date for all other deliverables is no later than '''Friday, December 18, 4:30pm''' (according to official final exam schedule for fall, 2015).
* The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on digital media to either Dr. Dahlquist or Dr. Dionisio.
* Each member of the group will be assigned the same grade for the group project.
* Detailed specifications, particularly for the [[Gene Database Project Deliverables#Group Report|group report]] and [[Gene Database Project Deliverables#Individual Assessment and Reflection|individual assessment and reflection]], are given on the [[Gene Database Project Deliverables]] page.

=== Group Deliverables ===

* 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]]
** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]
** 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'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=== Individual Deliverable ===

The individual deliverable is an [[Gene Database Project Deliverables#Individual Assessment and Reflection|assessment and reflection]] on the 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 and combined annotated bibliography (midnight 11/10)
* [[Week 11]] (midnight 11/17)
* [[Week 12]] (midnight 11/24)
* [[Week 14]] (midnight 12/8)
* [[Week 15]] (midnight 12/15)

== Groups ==

The project groups are:
# Team 1 - '''''Heavy Metal HaterZ''''' ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
#* Project Manager: Ron Legaspi
# Team 2 - '''Class Whoopers''' ''Bordetella pertussis'' (Whooping Cough)
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
#* Project Manager: Nicole Anguiano
# Team 3 - '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
#* Project Manager: Anu Varshneya
# Team 4 - ''' Oregon Trail Survivors''' ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristin Zebrowski
#* Project Manager: Kristin Zebrowski

== 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 (see above).

=== [[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). His or her tasks generally correspond to the work done during the DNA microarray analysis exercise ([http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1], [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]), as applicable to the team’s chosen bacterium.

=== [[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, Microsoft Excel, 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, version control, some troubleshooting, some programming. He or she coordinates with Drs. Dahlquist and Dionisio in extending GenMAPP Builder code and making new versions. GenMAPP Builder is written in Java and is built on open source pure-Java libraries. Source code is hosted on GitHub and built using Apache’s ''ant'' utility.

== 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.png|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://geneontology.org/page/download-ontology#Legacy_Downloads 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]]

{{Gene Database Project Links}}

[[Category:Group Projects]]

Gene Database Project Deliverables

2015-12-01T23:41:04Z

Kdahlquist: /* Group Files and Datasets */ linked to readme in markdown

{{Gene Database Project Links}}

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

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

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== 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:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
</gallery>

* 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 from your [[Week 11|journal club outline and presentation]].
* 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.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.
# 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 a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
* Gene Database Schema figure
* Gene Database Testing Report on final version of Gene Database (can be put at the end of the report as an Appendix)
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
*** Write a paragraph interpreting the GO results in light of the experiment performed in the published paper.
** 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.
** In particular, compare directly the log fold change value of a couple of key genes mentioned in the paper with what you found for those genes.
** Compare the criteria the journal article used for a significant expression change to the criteria that you used. How many genes met the criterion for the article vs. how many met the criterion for your analysis.

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings.
* How closely do your findings correspond to the original study?
* Are there significant differences?
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 18 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
# Background on your species and your species' genome from the genome paper presentation.
# The results of the Gene Database creation
#* Gene Database Schema figure
#* A table that summarizes how many OrderedLocusNames IDs were found
#** by XMLPipeDB match in the UniProt XML file
#** by TallyEngine in the UniProt XML file
#** by TallyEngine in the PostgreSQL database
#** in the OriginalRowCounts table in the gdb
#** in your external model organism database source
#* Give the command used in match to generate these results
#* Give the query used in PGAdmin III to generate these results
#* Include a screenshot of the TallyEngine results as a figure
#* Report on quantity and identity of gene IDs that did not make it into the database
#*# OrderedLocusNames IDs that were not in the XML source at all
#*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
#*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
#* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
# Introduce the experiment performed in the microarray paper, including the experimental design flow chart
# Report results of the DNA microarray analysis
#* Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
#* Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
#* Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
#** Show a list of 15-20 non-redundant GO terms.
#** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
#* GenMAPP MAPP of a pathway relevant to your results
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, December 15.'''''
** 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 evaluated by the instructors using the [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Group Files and Datasets ==

* 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]]
** [https://github.com/lmu-bioinformatics/xmlpipedb/blob/readme/GenMAPP%20Gene%20Databases/V.%20cholerae/V.%20cholerae%2020101022/ReadMe.md Sample ReadMe in markdown (a work in progress)]
** 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'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

== 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 or as a Word document uploaded to your group deliveables 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?

{{Gene Database Project Links}}

[[Category:Group Projects]]

Gene Database Project Deliverables

2015-12-01T22:09:17Z

Kdahlquist: /* PowerPoint Presentation */ organized list of stuff

{{Gene Database Project Links}}

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

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

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== 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:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
</gallery>

* 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 from your [[Week 11|journal club outline and presentation]].
* 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.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.
# 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 a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
* Gene Database Schema figure
* Gene Database Testing Report on final version of Gene Database (can be put at the end of the report as an Appendix)
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
*** Write a paragraph interpreting the GO results in light of the experiment performed in the published paper.
** 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.
** In particular, compare directly the log fold change value of a couple of key genes mentioned in the paper with what you found for those genes.
** Compare the criteria the journal article used for a significant expression change to the criteria that you used. How many genes met the criterion for the article vs. how many met the criterion for your analysis.

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings.
* How closely do your findings correspond to the original study?
* Are there significant differences?
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 18 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
# Background on your species and your species' genome from the genome paper presentation.
# The results of the Gene Database creation
#* Gene Database Schema figure
#* A table that summarizes how many OrderedLocusNames IDs were found
#** by XMLPipeDB match in the UniProt XML file
#** by TallyEngine in the UniProt XML file
#** by TallyEngine in the PostgreSQL database
#** in the OriginalRowCounts table in the gdb
#** in your external model organism database source
#* Give the command used in match to generate these results
#* Give the query used in PGAdmin III to generate these results
#* Include a screenshot of the TallyEngine results as a figure
#* Report on quantity and identity of gene IDs that did not make it into the database
#*# OrderedLocusNames IDs that were not in the XML source at all
#*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
#*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
#* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
# Introduce the experiment performed in the microarray paper, including the experimental design flow chart
# Report results of the DNA microarray analysis
#* Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
#* Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
#* Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
#** Show a list of 15-20 non-redundant GO terms.
#** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
#* GenMAPP MAPP of a pathway relevant to your results
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, December 15.'''''
** 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 evaluated by the instructors using the [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Group Files and Datasets ==

* 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'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

== 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 or as a Word document uploaded to your group deliveables 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?

{{Gene Database Project Links}}

[[Category:Group Projects]]

Gene Database Project Deliverables

2015-12-01T22:05:26Z

Kdahlquist: /* PowerPoint Presentation */ pasted in list from group report

{{Gene Database Project Links}}

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

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

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== 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:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
</gallery>

* 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 from your [[Week 11|journal club outline and presentation]].
* 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.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.
# 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 a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
* Gene Database Schema figure
* Gene Database Testing Report on final version of Gene Database (can be put at the end of the report as an Appendix)
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
*** Write a paragraph interpreting the GO results in light of the experiment performed in the published paper.
** 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.
** In particular, compare directly the log fold change value of a couple of key genes mentioned in the paper with what you found for those genes.
** Compare the criteria the journal article used for a significant expression change to the criteria that you used. How many genes met the criterion for the article vs. how many met the criterion for your analysis.

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings.
* How closely do your findings correspond to the original study?
* Are there significant differences?
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 18 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
* Background on your species and your species' genome from the genome paper presentation.
* Gene Database Schema figure
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
** GenMAPP MAPP of a pathway relevant to your results

* '''''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 17, even if you are presenting the following week.'''''
** 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 [[Presentation Rubric]].
* 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 organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Group Files and Datasets ==

* 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'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

== 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 or as a Word document uploaded to your group deliveables 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?

{{Gene Database Project Links}}

[[Category:Group Projects]]

Week 15

2015-12-01T21:54:27Z

Kdahlquist: removed under construction template

'''This journal entry is due on Tuesday, December 15, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The purpose of this assignment is to complete the team projects.
* The individual journal assignment (the electronic laboratory notebook) is due at midnight on Tuesday, December 15 and is worth 10 points.
* The team journal assignment is due at midnight on Tuesday, December 15 and is worth 3 points.
* The team [[Gene_Database_Project_Deliverables#PowerPoint_Presentation | PowerPoint presentation]] slides are due at midnight on Tuesday, December 15. The presentation will be delivered during the final exam period on Tuesday 2:00-4:00 PM. The final presentation is worth 45 points.
* The [[Gene_Database_Project_Deliverables#Group_Files_and_Datasets | deliverables]], [[Gene_Database_Project_Deliverables#Group_Report | Group Report]], and [[Gene_Database_Project_Deliverables#Individual_Assessment_and_Reflection | individual assessment and reflection]] are due by 4:30 PM on Friday, December 18. These are worth 175 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
* Clearly organize the deliverables page for your team (or alternately provide them on portable media, like a CD) by the final deadline of Friday, December 18, 4:30 PM.

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

Week 15

2015-12-01T21:54:05Z

Kdahlquist: /* Overview */ link to powerpoint presentation

'''This journal entry is due on Tuesday, December 15, at midnight PST.''' ''(Monday night/Tuesday morning)''

{{ Under Construction }}

== Overview ==

The purpose of this assignment is to complete the team projects.
* The individual journal assignment (the electronic laboratory notebook) is due at midnight on Tuesday, December 15 and is worth 10 points.
* The team journal assignment is due at midnight on Tuesday, December 15 and is worth 3 points.
* The team [[Gene_Database_Project_Deliverables#PowerPoint_Presentation | PowerPoint presentation]] slides are due at midnight on Tuesday, December 15. The presentation will be delivered during the final exam period on Tuesday 2:00-4:00 PM. The final presentation is worth 45 points.
* The [[Gene_Database_Project_Deliverables#Group_Files_and_Datasets | deliverables]], [[Gene_Database_Project_Deliverables#Group_Report | Group Report]], and [[Gene_Database_Project_Deliverables#Individual_Assessment_and_Reflection | individual assessment and reflection]] are due by 4:30 PM on Friday, December 18. These are worth 175 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
* Clearly organize the deliverables page for your team (or alternately provide them on portable media, like a CD) by the final deadline of Friday, December 18, 4:30 PM.

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

Gene Database Project

2015-12-01T21:53:31Z

Kdahlquist: /* Deliverables */ link to powerpoint presentation

{{Gene Database Project Links}}

== Deliverables ==

* You will give a final group [[Gene_Database_Project_Deliverables#PowerPoint_Presentation | PowerPoint presentation]] in class during the final exam period on '''Tuesday, December 15, 2:00pm'''.
* Final due date for all other deliverables is no later than '''Friday, December 18, 4:30pm''' (according to official final exam schedule for fall, 2015).
* The deliverables should be uploaded and organized onto one group wiki page, or alternately, delivered on digital media to either Dr. Dahlquist or Dr. Dionisio.
* Each member of the group will be assigned the same grade for the group project.
* Detailed specifications, particularly for the [[Gene Database Project Deliverables#Group Report|group report]] and [[Gene Database Project Deliverables#Individual Assessment and Reflection|individual assessment and reflection]], are given on the [[Gene Database Project Deliverables]] page.

=== Group Deliverables ===

* 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'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

=== Individual Deliverable ===

The individual deliverable is an [[Gene Database Project Deliverables#Individual Assessment and Reflection|assessment and reflection]] on the 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 and combined annotated bibliography (midnight 11/10)
* [[Week 11]] (midnight 11/17)
* [[Week 12]] (midnight 11/24)
* [[Week 14]] (midnight 12/8)
* [[Week 15]] (midnight 12/15)

== Groups ==

The project groups are:
# Team 1 - '''''Heavy Metal HaterZ''''' ''Shewanella oneidensis''
#* Coder: Mary Alverson
#* Quality Assurance: Josh Kuroda
#* GenMAPP Users: Ron Legaspi & Emily Simso
#* Project Manager: Ron Legaspi
# Team 2 - '''Class Whoopers''' ''Bordetella pertussis'' (Whooping Cough)
#* Coder: Nicole Anguiano
#* Quality Assurance: Brandon Klein
#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
#* Project Manager: Nicole Anguiano
# Team 3 - '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
#* Coder: Anu Varshneya
#* Quality Assurance: Brandon Litvak
#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
#* Project Manager: Anu Varshneya
# Team 4 - ''' Oregon Trail Survivors''' ''Shigella flexneri''
#* Coder: Jake Woodlee
#* Quality Assurance: Trixie Roque
#* GenMAPP Users: Erich Yanoschik & Kristin Zebrowski
#* Project Manager: Kristin Zebrowski

== 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 (see above).

=== [[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). His or her tasks generally correspond to the work done during the DNA microarray analysis exercise ([http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1], [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2]), as applicable to the team’s chosen bacterium.

=== [[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, Microsoft Excel, 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, version control, some troubleshooting, some programming. He or she coordinates with Drs. Dahlquist and Dionisio in extending GenMAPP Builder code and making new versions. GenMAPP Builder is written in Java and is built on open source pure-Java libraries. Source code is hosted on GitHub and built using Apache’s ''ant'' utility.

== 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.png|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://geneontology.org/page/download-ontology#Legacy_Downloads 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]]

{{Gene Database Project Links}}

[[Category:Group Projects]]

Gene Database Project Deliverables

2015-12-01T21:52:40Z

Kdahlquist: added section for PowerPoint presentation

{{Gene Database Project Links}}

== Group Report ==

These guidelines are based on the [https://peerj.com/about/author-instructions/ Instructions for Authors] issued by the [https://peerj.com/computer-science/ PeerJ Computer Science] journal. We have made this choice so that, if a group report is considered to be of sufficient quality, we can pursue publication of this report in ''PeerJ Computer Science'' as smoothly as possible. If there are formatting or detail questions that are not covered here, visit the [https://peerj.com/about/author-instructions/ Instructions for Authors] and follow their guidance.

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

=== Style Sheet ===

Use the following guidelines when formatting your report:
* 2.54 cm (1 in) margins on all sides
* Double-spaced
* 12 point Times/Times New Roman font
* Number the pages on the lower-right corner
* Use left justification (“jagged” on the right side)

=== Cover Page ===

Include the following information in a standalone cover page:
* A descriptive title for your project
** The function of the title is to identify the main result or take-home message of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?
* The names of the team members (with middle initials)
* The course number and title of the class
* The date of submission

=== Abstract ===

Provide an abstract of no more than 500 words.

=== 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:

<gallery mode="nolines" widths=322px heights=256px>
Funnel.png
</gallery>

* 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 from your [[Week 11|journal club outline and presentation]].
* 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.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.
# 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 a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
* Gene Database Schema figure
* Gene Database Testing Report on final version of Gene Database (can be put at the end of the report as an Appendix)
* A table that summarizes how many OrderedLocusNames IDs were found
** by XMLPipeDB match in the UniProt XML file
** by TallyEngine in the UniProt XML file
** by TallyEngine in the PostgreSQL database
** in the OriginalRowCounts table in the gdb
** in your external model organism database source
* Give the command used in match to generate these results
* Give the query used in PGAdmin III to generate these results
* Include a screenshot of the TallyEngine results as a figure
* Report on quantity and identity of gene IDs that did not make it into the database
*# OrderedLocusNames IDs that were not in the XML source at all
*# OrderedLocusNames IDs that were in the XML source but did not get imported into Postgres
*# OrderedLocusNames IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
* Report on what changes were made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs and the result of those changes
* Report results of the DNA microarray analysis
** Include a table that shows the results of your "Sanity Check", i.e., how many genes were significantly increased and decreased at different p value cut-offs in the dataset?
** Include the criteria you used for a significant increase and decrease in expression for your GenMAPP Expression Dataset
** Table of filtered MAPPFinder results (from ''.xls'' or ''.xls'')
*** Show a list of 15-20 non-redundant GO terms.
*** Include in your table the GO ID, the name of the GO term, the number changed/number present and the percent (e.g., 10/20 (50%)), the number present/number in GO and the percent, the regular p value and adjusted p value.
*** Write a paragraph interpreting the GO results in light of the experiment performed in the published paper.
** 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.
** In particular, compare directly the log fold change value of a couple of key genes mentioned in the paper with what you found for those genes.
** Compare the criteria the journal article used for a significant expression change to the criteria that you used. How many genes met the criterion for the article vs. how many met the criterion for your analysis.

=== Conclusions ===

Write a concluding paragraph that summarizes the overall project and your findings.
* How closely do your findings correspond to the original study?
* Are there significant differences?
* Did you discover anything new?
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

Write a short paragraph acknowledging the assistance of anyone who is not a member of your team.

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2015_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using [https://peerj.com/about/author-instructions/#reference-format PeerJ’s recommended reference format]. This format is very similar to APA style and should feel familiar if you have written research papers before.
* To minimize busy work, the PeerJ website includes links to downloadable style files for [https://www.zotero.org/styles/?q=peerj Zotero] and [http://endnote.com/downloads/style/peerj EndNote], if you use either system for managing and rendering references.

== PowerPoint Presentation ==

== Group Files and Datasets ==

* 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'' or ''.xlsx'')
* Data file used for import into GenMAPP (''.txt'' or ''.csv'')
* GenMAPP Expression Dataset file (''.gex'')
* Exceptions file of data imported into GenMAPP (''.EX.txt'')
* Raw MAPPFinder results files (''-GO.txt'')
* ''.gmf'' file
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

== 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 or as a Word document uploaded to your group deliveables 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?

{{Gene Database Project Links}}

[[Category:Group Projects]]

Week 15

2015-12-01T21:51:44Z

Kdahlquist: /* Overview */ added links to deliverables

'''This journal entry is due on Tuesday, December 15, at midnight PST.''' ''(Monday night/Tuesday morning)''

{{ Under Construction }}

== Overview ==

The purpose of this assignment is to complete the team projects.
* The individual journal assignment (the electronic laboratory notebook) is due at midnight on Tuesday, December 15 and is worth 10 points.
* The team journal assignment is due at midnight on Tuesday, December 15 and is worth 3 points.
* The team PowerPoint presentation slides are due at midnight on Tuesday, December 15. The presentation will be delivered during the final exam period on Tuesday 2:00-4:00 PM. The final presentation is worth 45 points.
* The [[Gene_Database_Project_Deliverables#Group_Files_and_Datasets | deliverables]], [[Gene_Database_Project_Deliverables#Group_Report | Group Report]], and [[Gene_Database_Project_Deliverables#Individual_Assessment_and_Reflection | individual assessment and reflection]] are due by 4:30 PM on Friday, December 18. These are worth 175 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
* Clearly organize the deliverables page for your team (or alternately provide them on portable media, like a CD) by the final deadline of Friday, December 18, 4:30 PM.

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

Week 15

2015-12-01T21:49:53Z

Kdahlquist: /* Team Journal Assignment */ prepare deliverables

'''This journal entry is due on Tuesday, December 15, at midnight PST.''' ''(Monday night/Tuesday morning)''

{{ Under Construction }}

== Overview ==

The purpose of this assignment is to complete the team projects.
* The individual journal assignment (the electronic laboratory notebook) is due at midnight on Tuesday, December 15 and is worth 10 points.
* The team journal assignment is due at midnight on Tuesday, December 15 and is worth 3 points.
* The team PowerPoint presentation slides are due at midnight on Tuesday, December 15. The presentation will be delivered during the final exam period on Tuesday 2:00-4:00 PM. The final presentation is worth 45 points.
* The deliverables, Group Report, and individual assessment and reflection are due by 4:30 PM on Friday, December 18. These are worth 175 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
* Clearly organize the deliverables page for your team (or alternately provide them on portable media, like a CD) by the final deadline of Friday, December 18, 4:30 PM.

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

Week 15

2015-12-01T21:48:07Z

Kdahlquist: /* Team Journal Assignment */ fixed typo

'''This journal entry is due on Tuesday, December 15, at midnight PST.''' ''(Monday night/Tuesday morning)''

{{ Under Construction }}

== Overview ==

The purpose of this assignment is to complete the team projects.
* The individual journal assignment (the electronic laboratory notebook) is due at midnight on Tuesday, December 15 and is worth 10 points.
* The team journal assignment is due at midnight on Tuesday, December 15 and is worth 3 points.
* The team PowerPoint presentation slides are due at midnight on Tuesday, December 15. The presentation will be delivered during the final exam period on Tuesday 2:00-4:00 PM. The final presentation is worth 45 points.
* The deliverables, Group Report, and individual assessment and reflection are due by 4:30 PM on Friday, December 18. These are worth 175 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).

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

Week 15

2015-12-01T21:47:50Z

Kdahlquist: changed shared to team

'''This journal entry is due on Tuesday, December 15, at midnight PST.''' ''(Monday night/Tuesday morning)''

{{ Under Construction }}

== Overview ==

The purpose of this assignment is to complete the team projects.
* The individual journal assignment (the electronic laboratory notebook) is due at midnight on Tuesday, December 15 and is worth 10 points.
* The team journal assignment is due at midnight on Tuesday, December 15 and is worth 3 points.
* The team PowerPoint presentation slides are due at midnight on Tuesday, December 15. The presentation will be delivered during the final exam period on Tuesday 2:00-4:00 PM. The final presentation is worth 45 points.
* The deliverables, Group Report, and individual assessment and reflection are due by 4:30 PM on Friday, December 18. These are worth 175 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).

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

Week 15

2015-12-01T21:46:28Z

Kdahlquist: /* Overview */ points and due dates

'''This journal entry is due on Tuesday, December 15, at midnight PST.''' ''(Monday night/Tuesday morning)''

{{ Under Construction }}

== Overview ==

The purpose of this assignment is to complete the team projects.
* The individual journal assignment (the electronic laboratory notebook) is due at midnight on Tuesday, December 15 and is worth 10 points.
* The team journal assignment is due at midnight on Tuesday, December 15 and is worth 3 points.
* The team PowerPoint presentation slides are due at midnight on Tuesday, December 15. The presentation will be delivered during the final exam period on Tuesday 2:00-4:00 PM. The final presentation is worth 45 points.
* The deliverables, Group Report, and individual assessment and reflection are due by 4:30 PM on Friday, December 18. These are worth 175 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Shared Journal Assignment ==

* Store your journal entry in the shared [[Class Journal Week 15]] page. If this page does not exist yet, go ahead and create it (congratulations on getting in first ''':)''' )
* Link to your journal entry from your user page.
* Link back from the journal entry to your user page.
**'''''NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.'''''
* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

[[Category:Assignment]]

Week 14

2015-12-01T21:35:07Z

Kdahlquist: /* Team Journal Assignment */ added reflection

'''This journal entry is due on Tuesday, December 8, at midnight PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The purpose of this assignment is to continue to make progress on the final projects. There are only two weeks left in the semester to complete the projects!
* Coders/Quality Assurance should analyze the initial exports and make any necessary changes to the custom species profile to capture all of the IDs for your species.
* GenMAPP Users should complete the statistical analysis of the microarray data, import the data into GenMAPP, and run MAPPFinder.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 14" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

== Team Journal Assignment ==

* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).

=== 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]]