LMU BioDB 2017 - User contributions [en]

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2017-12-18T20:14:50Z

Kdahlquist: /* Announcements */ delete 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 2017</div>

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

== Announcements ==

=== Upcoming Seminars ===

There are no further seminars for the remainder of the semester.

=== Undergraduate Library Research Award ===

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

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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/15)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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 (usually 10 points each)
| style="text-align: right" | 150
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (usually 3 points each)
| style="text-align: right" | 51
| points
|-
| Oral presentations
| style="text-align: right" | 120
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 100
| points
|-
| '''Total'''
| style="text-align: right" | '''421'''
| '''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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Main Page

2017-12-11T20:24:28Z

Kdahlquist: /* Part 3: Integrating for Research (GRNsight integration) */ fixed week 15 journal deadline

__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 2017</div>

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

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

There are no further seminars for the remainder of the semester.

=== Undergraduate Library Research Award ===

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

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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/15)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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 (usually 10 points each)
| style="text-align: right" | 150
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (usually 3 points each)
| style="text-align: right" | 51
| points
|-
| Oral presentations
| style="text-align: right" | 120
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 100
| points
|-
| '''Total'''
| style="text-align: right" | '''421'''
| '''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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

User talk:Dbashour

2017-12-09T18:58:46Z

Kdahlquist: note about input file

Dina, here is the new input file: [[Media:15-genes 32-edges team-hAPI Sigmoid estimation.xlsx | 15-genes 32-edges team-hAPI Sigmoid estimation.xlsx]]. I ran it on one of the computers in Seaver 120 in the back row. I left a note with your name on it there. The files will be on the T: drive in a folder called "Dina". I reduced the size of the network for the input file because it was too big. You will need to view it in GRNsight again. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:58, 9 December 2017 (PST)''

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time. You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# You forgot to invoke your template on the page, so you were missing the link to the assignment page and your category. The link to your user page was only present in your signature.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving files, please record the actual filename in your notebook for reference.
#* The name of your PowerPoint file was very generic and did not specify your initials or the strain you worked with.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Gln3 transcription factor.
# There was no summary paragraph. In particular, items 3-5 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as the GO term definitions. Please use the full APA format for citations in your references section.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:55, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Great!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the possibility that the '''data/Gene''' web service request might return more than one result (e.g., BRO1). In this case, since you know that you are working with SGD, you will want to pick the entry whose <code>primaryIdentifier</code> property looks like an SGD ID (that is, <code>S#########</code>).

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:01, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# You copied the methods from the Week 8 page and made some changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Since this is recording what you did, the language should be in the past tense.
#* You replaced all STRAIN references with "dGLN3", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references.
#* When the instructions say "repeat for all timepoints" you also need to provide the formulas for those because the cell references will change.
# At the top of your notebook, you did not record your strain, nor the number of replicates per timepoint.
# The number of replacements of "NA" was also not recorded.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADH1'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the magnitude of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. In your dataset, ''NSR1'' has an unadjusted p value < 0.05, but is no longer significant with the corrections. This means that we have some confidence that is is really changing in this experiment, but not as much as some other genes.
#* None of the ''ADH1'' p values are < 0.05, so the Average Log Fold Changes you see are likely just noise.
#* Also note that p values are between 0 and 1, which is why we use the "IF" statement to clear that up. For both genes, you should just report 1 for the Bonferroni p value.
# Your concluding paragraph is not sufficient. You need to summarize the purpose of this analysis, what you did, and your main results, both in terms of the numbers of genes significant and the specific ''NSR1'' and ''ADH1'' values., but you need to include the interpretation of the p values of ''NSR1'' and ''HSF1'' as noted above.
# Instead of having a separate section to report the answers to the questions, it would be better to just answer them at the point in which they appear in the protocol.
# This ''entire'' wiki page is your electronic notebook. The extra section you wrote, more properly belongs in the Acknowledgments section where you describe how you and Zach worked together.
# Finally, you also need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 21:29, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “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 organize your work and 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.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:20, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:06, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows a moderate level of detail.
* All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of a fixed nav is noted as the other “advanced Bootstrap” feature.
* The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
* The JSON API adaptation was not seen.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on computer science is noted; I agree with your sentiment that no knowledge is wasted knowledge in this regard. For you, although you are unlikely to write computer code in the future, the hope is that you walk away from this class with enough good exposure to coding that it influences how you think and approach problems, computer-related or not. This is where your exposure to programming and code might make you tackle a problem with greater rigor or precision.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:05, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:00, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** Punctuality took a hit, with 3 out of 7 listed edits coming after 12:01am, the last one being at 2:43pm
** On the bright side, 7 edits is a good number for this size journal, and you added summary entries to all of them
* Your lab notebook has very good detail, written in chronological log style, with a good focus on content acquisition

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here!
** Note that the standard library you used here does have a name: Bootstrap
** Indeed the flip side of widespread information availability is the loss of privacy and potential stealing of information

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* The HTML filename ended with two ''.html''s (''index.html.html'')—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
* A separate gene summary paragraph was not seen
* The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
* The Ensembl link does not go where it should (in fact it appears to be an error page)
* For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
* Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., ''S. cerevisiae'')
* The [[Week 4]] assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:19, 2 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in terms of providing feedback on the [[Week 3]] Assignment before I added my feedback on [[Week 2]] :) It looks like you addressed some of the issues I list below in your Week 2 journal entry, but here is the feedback anyway.
* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 13 of 27 saves (48%) in the period of review. Remember we are aiming for 100%
* However, the number of total saves on your individual wiki page is quite small (only 4). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Technically, you should have given the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
** Also, there appeared to be a spell check problem--"complementary" was given as "contemporary".
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* Your Acknowledgments section is missing your wiki signature.
* In your References section, you need to change the citation to the Week 2 assignment.
* I also note that the links to and from your User page to the journal entry and assignment are formatted as external links. Please be sure to follow the correct syntax for internal wiki links versus external links. Please remove the "Journal entries" category and just keep the "Journal Entry" category.
* My apologies for not getting to discussing "transcriptomes" and "proteomes" in class. We will be picking up those topics in the next week or two. In brief, a transcriptome refers to all of the mRNAs found in a cell at a given time and a protein refers to all of the proteins in a cell at a particular time. The difference is looking at one mRNA or proteina, versus all of them.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:32, 23 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits.
* You supplied an electronic notebook with this assignment, and it provided some good details in the spirit of openness and reproducibility, the values that we are after here. Keep it up, and always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, with your hacked headline fitting with the background image quite nicely!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted above, there were other IDs on this page beyond those kinds.
* There were a couple of small glitches in your acknowledgments and references: first, the signature should follow your statement about your work in the acknowledgments; in this journal page it appears after the references. And speaking of the references, the assignment reference still says “Week 1” rather than “Week 3.”
* Your shared journal’s chosen quote reflects an unfortunate tendency in computer science, which is the proliferation of jargon. I agree with your sentiments. Here’s hoping that we produce better-trained practitioners who will put more thought into the names that they choose!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:02, 23 September 2017 (PDT)

== Week 1 Feedback ==

* You completed most of your assignment on time, but we note that you did make some changes after the deadline, including your shared journal assignment and posting questions to myself and Dr. Dionisio’s talk pages.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** You included your off-campus residence address on the page to fulfill the requirement for a “snail mail” address. However, to protect your privacy, we suggest that you replace this with the “1 LMU Drive…” general campus address.
** You wrote something in the summary field for 10 of 13 saves, or 77%. We would like to see this approach 100%.
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please provide a link to an external website on your User page. This could be to the LMU home page or to some other organization you wish to highlight, for example.
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====.
** One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. Please go back and remove the lines in between, so that the numbered lines appear correctly. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
** You created a link to a file you intended to provide on your page, but the file itself was never uploaded to the wiki. Just like with images, it is a two-step process to upload the file and then to link to it on your page.
** Please use the category “Journal Entry” instead of the one you used, including it on your template.
** In a comment, you said you used Eddie Bachoura's page as inspiration. You actually need to say this visibly in your Acknowledgments section; this is the type of thing that we mean needs to go in this section.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 12 September 2017 (PDT)''

File:15-genes 32-edges team-hAPI Sigmoid estimation.xlsx

2017-12-08T23:53:01Z

Kdahlquist: Dina's input file

Dina's input file

GRNsight Gene Page Project Deliverables

2017-12-08T21:55:46Z

Kdahlquist: /* Group Report */ finished modifications to group report

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=== Grading ===

* The Group Report is worth 50 points.
* The Group PowerPoint presentation is worth 50 points.
* All other deliverables listed above, together, are worth 50 points.

== Group Report ==

Image of updated outline for Group Report
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:58, 7 December 2017 (PST) <br>
[[File:Biological databases paper outline.jpg | 500px]]



These guidelines have been modified based on discussion with the Project Managers in class on Thursday, December 7 and shown in the image above.

* 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)

=== Title Page ===

Include the following information in a standalone title 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. 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 ===

<s>Provide an abstract of no more than 500 words.</s> ''An abstract is no longer required.''

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be <s>3-5</s> '''1-2''' pages long (double-spaced). 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
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page 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 GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== Combined Materials & Methods/Results/Discussion section ===

This section will summarize the entire workflow and findings for the project with contributions from all team members, with subsections for the Data Analyst, QA/PM, and Coders. This needs to be a '''''narrative description''''' of what your team actually did, illustrated by figures and tables, as appropriate.
* Optional: create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text.
* 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.

==== Data Analyst ====

* Table of ANOVA results from the [[Week 8]], discussing the interpretation of the p values.
* From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the [[Week 10]] journal assignment.
** Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
** Discuss what the p values for the cluster and for the GO term list mean.
** Discuss the biological interpretation of your GO terms.
* Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
** Describe how and why you and your partner chose these transcription factors for your network.
** Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
* Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
* Interpret the results of the model as visualized in GRNsight.

==== Coders ====

* Give a narrative description of the new features created by the Coders.
** Provide code snippets and/or screenshots to illustrate as necessary.

==== QA ====

* Describe the data selected from each database for the gene page and the rationale for its inclusion.
* Describe any other tasks undertaken by the QA.

=== Conclusions ===

* Write a '''1-2''' page conclusion that summarizes the overall project and your findings.
** Overall, what have you learned about the regulation of cold shock in yeast?
** How does the new gene page feature facilitate the data analysis?
** What future directions would you take if you were to continue this project?
** Relate the results of your project to the papers you presented for journal club in [[Week 11]] (Coders) and [[Week 12]] (Data Analyst/QA).
*** Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?

=== 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_Fall2017_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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== 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 12 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:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be 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.

== 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 your team’s portion of the GRNsight Gene Page 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?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

GRNsight Gene Page Project Deliverables

2017-12-08T21:52:59Z

Kdahlquist: /* Cover Page */ changed cover to title

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=== Grading ===

* The Group Report is worth 50 points.
* The Group PowerPoint presentation is worth 50 points.
* All other deliverables listed above, together, are worth 50 points.

== Group Report ==

Image of updated outline for Group Report
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:58, 7 December 2017 (PST) <br>
[[File:Biological databases paper outline.jpg | 500px]]



These guidelines have been modified based on discussion with the Project Managers in class on Thursday, December 7 and shown in the image above.

* 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)

=== Title Page ===

Include the following information in a standalone title 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. 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 ===

<s>Provide an abstract of no more than 500 words.</s> ''An abstract is no longer required.''

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be <s>3-5</s> '''1-2''' pages long (double-spaced). 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
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page 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 GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== Combined Materials & Methods/Results/Discussion section ===

This section will summarize the entire workflow and findings for the project with contributions from all team members, with subsections for the Data Analyst, QA/PM, and Coders. This needs to be a '''''narrative description''''' of what your team actually did, illustrated by figures and tables, as appropriate.
* Optional: create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text.
* 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.

==== Data Analyst ====

* Table of ANOVA results from the [[Week 8]], discussing the interpretation of the p values.
* From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the [[Week 10]] journal assignment.
** Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
** Discuss what the p values for the cluster and for the GO term list mean.
** Discuss the biological interpretation of your GO terms.
* Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
** Describe how and why you and your partner chose these transcription factors for your network.
** Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
* Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
* Interpret the results of the model as visualized in GRNsight.

==== Coders ====

* Give a narrative description of the new features created by the Coders.
** Provide code snippets and/or screenshots to illustrate as necessary.

==== QA ====

* Describe the data selected from each database for the gene page and the rationale for its inclusion.
* Describe any other tasks undertaken by the QA.

=== Discussion ===

* Overall, what have you learned about the regulation of cold shock in yeast?
* How does the new feature facilitate the data analysis?
* Relate the results of your project to the papers you presented for journal club in [[Week 11]] (Coders) and [[Week 12]] (Data Analyst/QA).
** Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* 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_Fall2017_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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== 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 12 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:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be 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.

== 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 your team’s portion of the GRNsight Gene Page 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?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

GRNsight Gene Page Project Deliverables

2017-12-08T21:52:16Z

Kdahlquist: /* Group Report */ continue to modify report

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=== Grading ===

* The Group Report is worth 50 points.
* The Group PowerPoint presentation is worth 50 points.
* All other deliverables listed above, together, are worth 50 points.

== Group Report ==

Image of updated outline for Group Report
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:58, 7 December 2017 (PST) <br>
[[File:Biological databases paper outline.jpg | 500px]]



These guidelines have been modified based on discussion with the Project Managers in class on Thursday, December 7 and shown in the image above.

* 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. 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 ===

<s>Provide an abstract of no more than 500 words.</s> ''An abstract is no longer required.''

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be <s>3-5</s> '''1-2''' pages long (double-spaced). 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
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page 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 GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== Combined Materials & Methods/Results/Discussion section ===

This section will summarize the entire workflow and findings for the project with contributions from all team members, with subsections for the Data Analyst, QA/PM, and Coders. This needs to be a '''''narrative description''''' of what your team actually did, illustrated by figures and tables, as appropriate.
* Optional: create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text.
* 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.

==== Data Analyst ====

* Table of ANOVA results from the [[Week 8]], discussing the interpretation of the p values.
* From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the [[Week 10]] journal assignment.
** Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
** Discuss what the p values for the cluster and for the GO term list mean.
** Discuss the biological interpretation of your GO terms.
* Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
** Describe how and why you and your partner chose these transcription factors for your network.
** Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
* Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
* Interpret the results of the model as visualized in GRNsight.

==== Coders ====

* Give a narrative description of the new features created by the Coders.
** Provide code snippets and/or screenshots to illustrate as necessary.

==== QA ====

* Describe the data selected from each database for the gene page and the rationale for its inclusion.
* Describe any other tasks undertaken by the QA.

=== Discussion ===

* Overall, what have you learned about the regulation of cold shock in yeast?
* How does the new feature facilitate the data analysis?
* Relate the results of your project to the papers you presented for journal club in [[Week 11]] (Coders) and [[Week 12]] (Data Analyst/QA).
** Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* 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_Fall2017_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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== 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 12 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:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be 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.

== 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 your team’s portion of the GRNsight Gene Page 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?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

GRNsight Gene Page Project Deliverables

2017-12-08T21:43:21Z

Kdahlquist: /* Abstract */ fix formatting

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=== Grading ===

* The Group Report is worth 50 points.
* The Group PowerPoint presentation is worth 50 points.
* All other deliverables listed above, together, are worth 50 points.

== Group Report ==

Image of updated outline for Group Report
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:58, 7 December 2017 (PST) <br>
[[File:Biological databases paper outline.jpg | 500px]]



These guidelines have been modified based on discussion with the Project Managers in class on Thursday, December 7 and shown in the image above.

* 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. 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 ===

<s>Provide an abstract of no more than 500 words.</s> ''An abstract is no longer required.''

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be <s>3-5</s> '''1-2''' pages long (double-spaced). 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
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page 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 GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== 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.

Create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text. You should provide citations to the individual electronic notebooks of the team members as appropriate in the text so that the reader knows where to go for additional details.

=== 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.

==== Results of Microarray Data Analysis ====

* Table of ANOVA results from the [[Week 8]], discussing the interpretation of the p values.
* From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the [[Week 10]] journal assignment.
** Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
** Discuss what the p values for the cluster and for the GO term list mean.
** Discuss the biological interpretation of your GO terms.
* Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
** Describe how and why you and your partner chose these transcription factors for your network.
** Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
* Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
* Interpret the results of the model as visualized in GRNsight.

==== Coding Results ====

* Give a narrative description of the new features created by the Coders.
** Provide code snippets and/or screenshots to illustrate as necessary.

=== Discussion ===

* Overall, what have you learned about the regulation of cold shock in yeast?
* How does the new feature facilitate the data analysis?
* Relate the results of your project to the papers you presented for journal club in [[Week 11]] (Coders) and [[Week 12]] (Data Analyst/QA).
** Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* 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_Fall2017_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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== 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 12 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:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be 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.

== 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 your team’s portion of the GRNsight Gene Page 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?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

GRNsight Gene Page Project Deliverables

2017-12-08T21:42:44Z

Kdahlquist: /* Group Report */ started to modify

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=== Grading ===

* The Group Report is worth 50 points.
* The Group PowerPoint presentation is worth 50 points.
* All other deliverables listed above, together, are worth 50 points.

== Group Report ==

Image of updated outline for Group Report
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:58, 7 December 2017 (PST) <br>
[[File:Biological databases paper outline.jpg | 500px]]



These guidelines have been modified based on discussion with the Project Managers in class on Thursday, December 7 and shown in the image above.

* 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. 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 ===

<s>Provide an abstract of no more than 500 words.</> ''An abstract is no longer required.''

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be <s>3-5</s> '''1-2''' pages long (double-spaced). 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
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page 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 GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== 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.

Create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text. You should provide citations to the individual electronic notebooks of the team members as appropriate in the text so that the reader knows where to go for additional details.

=== 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.

==== Results of Microarray Data Analysis ====

* Table of ANOVA results from the [[Week 8]], discussing the interpretation of the p values.
* From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the [[Week 10]] journal assignment.
** Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
** Discuss what the p values for the cluster and for the GO term list mean.
** Discuss the biological interpretation of your GO terms.
* Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
** Describe how and why you and your partner chose these transcription factors for your network.
** Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
* Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
* Interpret the results of the model as visualized in GRNsight.

==== Coding Results ====

* Give a narrative description of the new features created by the Coders.
** Provide code snippets and/or screenshots to illustrate as necessary.

=== Discussion ===

* Overall, what have you learned about the regulation of cold shock in yeast?
* How does the new feature facilitate the data analysis?
* Relate the results of your project to the papers you presented for journal club in [[Week 11]] (Coders) and [[Week 12]] (Data Analyst/QA).
** Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* 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_Fall2017_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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== 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 12 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:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be 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.

== 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 your team’s portion of the GRNsight Gene Page 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?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

File:17-genes 39-edges teamINT Sigmoid estimation.xlsx

2017-12-07T23:28:07Z

Kdahlquist: Kdahlquist uploaded a new version of File:17-genes 39-edges teamINT Sigmoid estimation.xlsx

complete GRNmap input file for Emma/Int&Int team

User talk:Mbalducc

2017-12-07T08:37:48Z

Kdahlquist: add link to GRNmap input file

Mary, I've made the GRNmap input file for use in class on Thursday: [[Media:17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx | 17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 00:37, 7 December 2017 (PST)''

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving files, please record the actual filename in your notebook for reference.
#* Be attentive to writing something in the summary field '''''every''''' time you make a change to the wiki.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Cin5 transcription factor.
# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to what is noted in number 2 above.
# The gene list and GO list files were provided (make sure that they have the correct file extensions). However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# The PowerPoint with the screenshots of the stem results was also not found. Without this, I was unable to really review your results. These screenshots will be included in your final presentation and report.
# You did not actually mention which profile you chose until the summary paragraph. This information is critical to your notebook. You reversed the number of genes that belonged to the profile versus expected. The profile you chose has a relatively small number of genes. It would be better to choose one of the profiles with at least 100 genes for the further analysis in the final project.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as each of the GO term definitions, not just the general Gene Ontology site.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:29, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “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 organize your work and 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.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:54, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are almost fulfilled and on-time. An unusually low subset of the listed submissions in the page’s history have a summary, 9/24.
* The electronic notebook has good detail and is clear in its bulleted form.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly, along with the portions to substitute depending on the desired gene as well as the overall process for going from the gene symbol to the final gene data.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:29, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made some changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Since this is recording what you did, the language should be in the past tense.
#* You provided the formulas that were specific to your dataset. However, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# At the top of the protocol, you recorded your strain, but did not record the number of replicates per timepoint.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and '''HSF1'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the magnitude of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. NSR1 has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
#* ''HSF1'' also shows some largish Average Log Fold Changes. But more importantly, its Benjamini and Hochberg p value is ~0.02, which is significant. So, you can conclude that it '''''is''''' changing expression due to cold shock.
# Your concluding paragraph is pretty good, but you need to include the interpretation of the p values of ''NSR1'' and ''HSF1'' as noted above. Also, you report the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:57, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the signature is missing from the acknowledgments section and the references are somewhat minimal—certainly more material was used in this assignment than just the instructions?
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
** The gene page does not have its own references section (separate from the one in your individual journal page).
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to see that the out-of-comfort exposure is looking just right for you. It is tricky to strike a balance between sufficient exposure to do something substantive alongside skipping some basics and practice in order to save time, but it's looking like the mix is generally OK for you except for the need for more practice.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:43, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:00, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Great work on your individual journal! All “good habit” items are addressed, it was submitted on time, you spaced your work out well (9 edits), and had summary entries for all of them.
* Your electronic notebook has sufficient detail and includes some very specific notes, giving it genuine individuality and keeping it from sounding like it could have been anyone else's process.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap
** Indeed the flip side of widespread information availability is the loss of privacy and potential misinformation

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I could record my feedback on [[Week 2]] :) In any event, here is the feedback.
* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 11 of 19 saves (58%) in the period of review. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 16, which is in the range of what was expected for this assignment.
* Your complementary DNA sequence was correct.
* Your +1, +2, frame translations were correct.
** There was a missing "T" in the +3 frame.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you need to change the citation to the Week 2 assignment.
* For your shared journal, the link from your user page to the shared journal page was missing.
* I also can't really visualize a hypercube; it is something that we can't render in 2D or 3D, I think. The current table form emphasizes how the third nucleotide can be redundant and degenerate. I think the other representation would help to understand how the first or second amino acid could be mutated an change the translation to a related amino acid.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:07, 23 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for 16 out of the 17 listed journal edits.
* You supplied an electronic notebook with this assignment, with the kinds of details that support openness and reproducibility, the values that we are after here. Look to try to answer these questions: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? In that spirit, one portion that could use more detail was the last portion, which you characterized as tricky. Digging into what made something tricky, or what you tried that didn’t work, can be just as helpful to readers of your notebook as talking about what did work.
* Your hack-a-page work certainly fulfilled the instructions, with a nice dash of humor (or is it satire?).
* Your list of links was quite thorough, and of course there are more where those came from.
* You correctly listed a subset of the IDs in the page, and in this case you took the most explicit ones, the element IDs. Note that there are other kinds of IDs in the page and I was hoping you would catch those as well—for example, each reading frame entry got its own ID.
* Your shared journal chosen quote is actually something I say a lot when I teach computer science courses—learning computer science takes away the “magic” that many people feel when faced with the wonders of technology. The hope, however, is that the knowledge behind the magic actually feels more fulfilling and empowering than the sense of magic itself.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 23 September 2017 (PDT)

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses.
** Please make an explicit statement about your career interests and goals.
** You wrote something in the summary field for 13 of 24 saves, or 54%. We would like to see this approach 100%.
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax, including your name on the Main page.
** You uploaded a file and linked to it on your page, but the name of the file is very generic “Resume.pdf” Someone else in the class could have uploaded a file with the same name and overwritten the file without your knowledge. Now is a good time to get into the habit of using more informative names for your files. Usually this includes your last name and the date, but could include the course, type of assignment, etc. This is especially important when you are posting or sending files via e-mail to another person.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” Please make this change, including it on your template, instead of on the User page itself.
** Also, you did not put the link to the Shared Journal page from your User page. Please include this link on your template as well. For each week, you will need to include links to the actual assignment page, your individual journal page, and the shared journal page from your user page (as well as the category). If you get into the habit of including this on your template, you will only need to edit once and all the pages will reflect the change. You can also go ahead and make your template for the rest of the semester so you will always have this part of the assignment fulfilled.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 12 September 2017 (PDT)''

File:17-genes 19-edges team-hAPI Sigmoid estimation.xlsx

2017-12-07T08:36:18Z

Kdahlquist: GRNmap input workbook for team hAPI: Mary

GRNmap input workbook for team hAPI: Mary

User talk:Emmatyrnauer

2017-12-07T08:13:53Z

Kdahlquist: add link to GRNmap input file

Emma, I've made the GRNmap input file based on your network for use in class on Thursday: [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 00:13, 7 December 2017 (PST)''

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. Because your B-H p value computations were incorrect in Week 8, you will need to redo the stem analysis. When you do, come back to edit this page and replace the results shown here with the new ones generated with the correct gene list. When you redo this, also pay attention to the feedback below, making the necessary changes. Your weekly electronic notebook for the project can then link to your Week 10 page, noting the corrections you made.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did. You do not need to include the "background" section here because it is not really part of anything that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving or opening files, please record the actual filename in your notebook for reference at the point in the protocol where it is mentioned.
# When you discussed why you chose the profile you did, you said the genes were down-regulated, but they are actually up-regulated in that profile.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock. Also, please include their GO IDs.
# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to cold shock in yeast.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as each of the GO term definitions, not just the general Gene Ontology site.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:49, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “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 organize your work and 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.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:59, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Thank you!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the last URL that delivers the full data for a single gene. After performing the needed '''esearch''' API calls, you want to make a final '''esummary''' API call in order to get the full dataset for the specific gene whose ID you were able to extract via '''esearch'''.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:41, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.
* Thank you for submitting the assignment on time.
* All required links were present on the page.
You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# You copied the methods from the [[Week 8]] page and made some changes to make them specific for what ''you'' did, but you needed to go further than you did with those changes.
#* Since this is recording what you ''did'', the language should be in the ''past'' tense.
#* You replaced all ''STRAIN'' references with "wt", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references.
# You have a typo for the number of genes that are p < 0.0001 in your PowerPoint slide.
# When reporting the percent of genes that are changed, only give 1 or 2 decimal places instead of 4.
# There is a mistake in the Benjamini-Hochberg p value computation.
#* You need to sort the unadjusted p values smallest to largest before assigning their rank and applying the formula. You just left them in the order of the Master Index, so all of the B-H p values will be wrong.
#* You need to redo this computation. Unfortunately, this also means that you will need to redo the stem clustering because it will have been based on the incorrect list of genes.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADA2'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the ''magnitude'' of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. ''NSR1'' has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
#* ''ADA2'' also shows some largish Average Log Fold Changes. But it has an unadjusted p value of ~0.008, which does not stay < 0.05 with either the Bonferroni and B-H corrections. We have less confidence that ''ADA2'' is really changing its expression because of the p value.
# Your summary paragraph is a good description of the flow of work for this week. However, it should draw some more conclusions based on the table of p values and be corrected to interpret the expression of ''NSR1'' and ''ADA2'' above.
#* In particular, do we know if genes are really changing expression, and how do we know it (hint: look at the percent of genes changed at each p value cut-off relative to the cut-off itself, e.g., p < 0.05 = 5%.)
# You included your Acknowledgments and References. However, you should have been more explicit in your Acknowledgments that you directly copied, then modified the Week 8 instructions. You also needed to Acknowledge the source of the data.

Please let me know if you have any questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:03, 15 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively narrated, and your references section thoughtfully includes the multiple sources you consulted for this assignment (although it appears to be missing the baseline reference for [[Week 7]]).
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of carousel is noted as the other “advanced Bootstrap” feature.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Yes, the coding can certainly be challenging and ideally would be given more practice time, but due to our time constraints we have to keep it in the "need-to-know/just-in-time" level. But that’s indeed why we have the mixed partners, so it’s good to hear that this helps you.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 14:32, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** Your folder name and name for your HTML file was based on your last names instead of the gene standard name as requested in the assignment.
** Your folder name and HTML filename should have been all lowercase letters.
** You provided the image in the folder, but did not delete the grnsight-screenshot.html which was not used in your page.
** Thank you for providing the in-text citations and references in APA format. However, because we have the power of HTML, it would have been nice to have URLs in the references provided as actual hyperlinks.
** I did not see an actual summary paragraph about your gene.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* The carousel option for your reviews of the individual databases was a nice touch. However, since the length of the content for each "slide" is different, the page "jumps" when the slide is advanced. It might also be nice to either set the view time for each slide to be longer or disable the auto-advance because I didn't have enough time to read each slide.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:40, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* Don't forget to invoke your template on your individual journal entry page--you were missing the link back to your User page because of it.
* Your electronic lab notebook had a moderate level of detail about what you did, but could have included some of the results as well, gene data and some examples of code that you used for your web page.
* You made a total of 21 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* You had a complete list of references in APA format, but since this is a wiki, please make the URLs hyperlinks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:00, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 18 of the listed journal edits.
* You supplied an electronic notebook with this assignment, separated into a ''Notebook'' subheading for each section; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…I’m pleasantly surprised that you didn’t encounter any issues with a Facebook image (note how I wouldn’t have known this if you hadn’t indicated as much in your notebook!). Sometimes they limit linkable items from their feeds; good that you weren’t bitten by that here.
* You identified a sufficient number and variety of links correctly, including the '''cgi-bin''' action that does the actual transcription/translation. This appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. It sounds like you aren’t deterred—don’t be! Indeed it is by continued exposure that you will gain the foundation you mentioned to increasingly make good use of the functions that are available to you on the command line.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:22, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but you changed 5' and 3' to N-ter and C-ter after the deadline.
* You wrote something in the summary field for 13 of 15 saves (87%) in the period of review, which is very good. Remember, we are aiming for 100%.
* The number of total saves to your Week 2 journal entry before the deadline was 10, which is just within the range for this assignment.
* You were missing the Category "Journal Entry", please add it to your template and invoke your template on future journal entries.
* You were also missing a link back to your User page, except in your wiki signature in the Acknowledgments. Please add this to your template if you have not already and invoke your template in future assignments.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you substituted a G for the second W in the -1 frame.
* Your determination of which frames contained ORFs was correct.
* One note I will make is that you reversed your labeling of the +1, +2, and +3 strands with -1, -2, and -3. It is the convention to call the top 5' to 3' ''DNA'' strand the (+) frames and the bottom 3' to 5' ''DNA'' strand the (-) frames. That is because we normally report gene sequences in the 5' to 3' direction, left to right, and the top-strand would be considered the "mRNA-like" strand because it is in that orientation.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* Not only do experimental descriptions use technical language, they presuppose familiarity with the procedures that those new to the field do not have. We assign this because, like with other fields of endeavor, it is good to take a look at the primary source. I can try to answer any specific questions you have, if you like.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 17:14, 21 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 20 edits were made to your user page—a good, gradual pace—but only around five of those had a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* Commented-out content (<code><nowiki></nowiki></code>) was not seen in your submission.
* You created a template correctly, but it is not used.

For your shared journal response, a link to the shared response from your user page was not seen. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:48, 11 September 2017 (PDT)

File:17-genes 39-edges teamINT Sigmoid estimation.xlsx

2017-12-07T08:12:00Z

Kdahlquist: complete GRNmap input file for Emma/Int&Int team

complete GRNmap input file for Emma/Int&Int team

User talk:Aporras1

2017-12-07T07:39:57Z

Kdahlquist: note that file is now complete for GRNmap

The file has now been completed for input to GRNmap in class on Thursday. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:39, 6 December 2017 (PST)''

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. I posted this on your Week 15 journal page as well. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:56, 6 December 2017 (PST)''

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is basically complete. One note is that when you talk about saving files, please record the actual filename in your notebook for reference.
# You did not report the definitions of your 6 GO terms.
# There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
# There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used. Eventually when you look up the GO term definitions, you will need to cite those pages as well.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time, and completely fulfilled. Great work!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all on-time, and mostly fulfilled (your shared entry does not have a wiki signature). Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:21, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Good work changing the instructions to the past tense. Make sure that this is followed through for the entire protocol.
#* You replaced all STRAIN references with "dZAP1", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references. In addition, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# Good job with reporting and interpreting the Average Log Fold Changes and p values for ''NSR1'' and ''CLN1''.
# Your concluding paragraph is very good. My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “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 organize your work and 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.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:10, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment about the computer science exposure being too far too fast is a side effect of the "just in time" learning structure of the class. It does result in a lighter treatment of certain topics and that's what I think you’re feeling. Basics coverage would have been great but it would have cost additional time. It’s a tradeoff that we’ve made consciously, but of course if you’re interested in additional details, feel free to come to office hours to talk about these things.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:23, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:22, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal was mostly on-time—35 edits’ worth!—with the last edit landing at 12:02am.
** But on a positive note, all 35 listed edits had a summary entry—keep that up!
** Your journal page still does not have a category—please put that in your template so that you don't have to worry about it again.
* Your lab notebook has some great detail, but remains quite easy to read and follow. This is great!
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

All questions and “good habit” points are fulfilled! And indeed the flip side of the Internet’s success is the danger and quality of our data. Vigilance for this can never let up.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, with comments on 16 out of the 17 listed journal edits in the history.
* Your journal entry page does not have a category—just put this in your template so you don’t forget.
* You supplied an electronic notebook with this assignment, with a fine level of detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** Note that we’ll want you to integrate your notebook right with your journal page from this point on, instead of a separate page like you have here.
* Your hack-a-page work certainly fulfilled the instructions; if only Fox News’s biggest headlines ''were'' about domesticated teddy bear hamsters!
* You listed a good number of links for a variety of resource types, so that works out nicely.
* Your list of IDs was also of decent size, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* Sorry to hear that you weren’t able to work out the “cleanup” commands. This might be good to follow-up on with your homework partner for this week, to make sure that you don’t miss out on the skills that the solution requires.
* Your shared journal entry and chosen quote actually speak to the heart of the “science” in “computer science”—''limits''. Theoretical computer science is very much about the limits of computation. As for how-to guidance, I’d say that office hours would be a great opportunity for getting that. I’ll be happy to review any of the technical content that you’ll see in the class.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:46, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 32 of 38 saves (84%) in the period of review, which is very good. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 18, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was your category. Please make sure that these are included in your template and that you invoke the template on each journal entry, if you haven't made this change already.
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:40, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* I don’t see an email from you regarding worries/concerns or additional information.
* You only went to two levels of depth with your headings; the instructions requested at least three levels.

None of these other items were found in your submission:
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Your answer to the first question after doing the readings. Unfortunately, it did not help that your answers were conflated into paragraph form, rather than a point-by-point Q&A. Implied answers were found to most of the questions, except for the first post-reading question.

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:42, 11 September 2017 (PDT)

File:15-gene 44-edge teamJASPAR Sigmoid estimation.xlsx

2017-12-07T07:38:39Z

Kdahlquist: Kdahlquist uploaded a new version of File:15-gene 44-edge teamJASPAR Sigmoid estimation.xlsx

adjusted network size for JASPAR team: Antonio

User talk:Aporras1

2017-12-06T23:56:39Z

Kdahlquist: note about file pared down and uploaded to Week 15 page

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. I posted this on your Week 15 journal page as well. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:56, 6 December 2017 (PST)''

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is basically complete. One note is that when you talk about saving files, please record the actual filename in your notebook for reference.
# You did not report the definitions of your 6 GO terms.
# There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
# There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used. Eventually when you look up the GO term definitions, you will need to cite those pages as well.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time, and completely fulfilled. Great work!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all on-time, and mostly fulfilled (your shared entry does not have a wiki signature). Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:21, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Good work changing the instructions to the past tense. Make sure that this is followed through for the entire protocol.
#* You replaced all STRAIN references with "dZAP1", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references. In addition, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# Good job with reporting and interpreting the Average Log Fold Changes and p values for ''NSR1'' and ''CLN1''.
# Your concluding paragraph is very good. My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “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 organize your work and 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.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:10, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment about the computer science exposure being too far too fast is a side effect of the "just in time" learning structure of the class. It does result in a lighter treatment of certain topics and that's what I think you’re feeling. Basics coverage would have been great but it would have cost additional time. It’s a tradeoff that we’ve made consciously, but of course if you’re interested in additional details, feel free to come to office hours to talk about these things.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:23, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:22, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal was mostly on-time—35 edits’ worth!—with the last edit landing at 12:02am.
** But on a positive note, all 35 listed edits had a summary entry—keep that up!
** Your journal page still does not have a category—please put that in your template so that you don't have to worry about it again.
* Your lab notebook has some great detail, but remains quite easy to read and follow. This is great!
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

All questions and “good habit” points are fulfilled! And indeed the flip side of the Internet’s success is the danger and quality of our data. Vigilance for this can never let up.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, with comments on 16 out of the 17 listed journal edits in the history.
* Your journal entry page does not have a category—just put this in your template so you don’t forget.
* You supplied an electronic notebook with this assignment, with a fine level of detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** Note that we’ll want you to integrate your notebook right with your journal page from this point on, instead of a separate page like you have here.
* Your hack-a-page work certainly fulfilled the instructions; if only Fox News’s biggest headlines ''were'' about domesticated teddy bear hamsters!
* You listed a good number of links for a variety of resource types, so that works out nicely.
* Your list of IDs was also of decent size, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* Sorry to hear that you weren’t able to work out the “cleanup” commands. This might be good to follow-up on with your homework partner for this week, to make sure that you don’t miss out on the skills that the solution requires.
* Your shared journal entry and chosen quote actually speak to the heart of the “science” in “computer science”—''limits''. Theoretical computer science is very much about the limits of computation. As for how-to guidance, I’d say that office hours would be a great opportunity for getting that. I’ll be happy to review any of the technical content that you’ll see in the class.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:46, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 32 of 38 saves (84%) in the period of review, which is very good. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 18, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was your category. Please make sure that these are included in your template and that you invoke the template on each journal entry, if you haven't made this change already.
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:40, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* I don’t see an email from you regarding worries/concerns or additional information.
* You only went to two levels of depth with your headings; the instructions requested at least three levels.

None of these other items were found in your submission:
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Your answer to the first question after doing the readings. Unfortunately, it did not help that your answers were conflated into paragraph form, rather than a point-by-point Q&A. Implied answers were found to most of the questions, except for the first post-reading question.

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:42, 11 September 2017 (PDT)

Aporras1 Week 15

2017-12-06T23:55:22Z

Kdahlquist: /* =SPT23 deletion */ added pared down file; fixed header level

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in folder "FOLDER NAME": Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in folder "FOLDER NAME": Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in folder "FOLDER NAME": Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in folder "FOLDER NAME": Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 15 and column O containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.

==References==
#LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
#LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

[[Category:Journal Entry]]

File:15-gene 44-edge teamJASPAR Sigmoid estimation.xlsx

2017-12-06T23:53:59Z

Kdahlquist: adjusted network size for JASPAR team: Antonio

adjusted network size for JASPAR team: Antonio

Main Page

2017-12-04T17:03:27Z

Kdahlquist: /* Upcoming Seminars */ no more seminars

__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 2017</div>

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

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

There are no further seminars for the remainder of the semester.

=== Undergraduate Library Research Award ===

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

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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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 (usually 10 points each)
| style="text-align: right" | 150
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (usually 3 points each)
| style="text-align: right" | 51
| points
|-
| Oral presentations
| style="text-align: right" | 120
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 100
| points
|-
| '''Total'''
| style="text-align: right" | '''421'''
| '''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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Main Page

2017-12-01T00:21:51Z

Kdahlquist: /* Course Work and Grading */ adjusted point totals based on actual grades given and plans for final project

__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 2017</div>

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

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 3'''
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium

=== Undergraduate Library Research Award ===

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

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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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 (usually 10 points each)
| style="text-align: right" | 150
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (usually 3 points each)
| style="text-align: right" | 51
| points
|-
| Oral presentations
| style="text-align: right" | 120
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 100
| points
|-
| '''Total'''
| style="text-align: right" | '''421'''
| '''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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

GRNsight Gene Page Project

2017-12-01T00:11:46Z

Kdahlquist: /* Common Deliverables */ added grading

{{GRNsight Gene Page Project Links}}

== Overall Project Goal ==

The GRNsight gene page project seeks to add significant functionality to GRNsight by allowing users to open a gene information page from a chosen gene in the currently displayed ''Saccharomyces cerevisiae'' gene regulation network. The gene information page shall open a new browser tab or window and display, in an informative and visually effective way, the information known about this gene based on five APIs: UniProt, Ensembl, SGD (YeastMine), NCBI, and JASPAR.

For this project, we shall restrict the current organism to just ''Saccharomyces cerevisiae''. Because GRNsight can be used to display GRNs from any species—and in fact to display graphs that are not GRNs at all—the gene page functionality shall be robust enough to handle non-''S. cerevisiae'' nodes in a graceful and informative manner.

To facilitate the development of the gene page, the class has been divided into four groups:
* Page Design
* Gene Database APIs
* JASPAR API
* Interaction and Integration

Each team is responsible for a specific portion of the overall gene page, detailed below. The members of each team will also have specific roles, also detailed below. Team members in a specific role are also expected to work with each other across teams as ''guilds'', in order to keep each component of the project coordinated and consistent.

== Common Deliverables ==

* You will give a final group [[GRNsight Gene Page Project Deliverables#PowerPoint_Presentation | PowerPoint presentation]] in class during the final exam period on '''Tuesday, December 12, 2:00pm'''.
* Final due date for all other deliverables is no later than '''Friday, December 15, 4:30pm''' (according to official final exam schedule for fall, 2017).
* 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 [[GRNsight Gene Page Project Deliverables#Group Report|group report]] and [[GRNsight Gene Page Project Deliverables#Individual Assessment and Reflection|individual assessment and reflection]], are given on the [[GRNsight Gene Page Project Deliverables]] page.
** The Group Report is worth 50 points.
** The Group PowerPoint presentation is worth 50 points.
** All other deliverables listed on the [[GRNsight Gene Page Project Deliverables | Deliverables]] page, together, are worth 50 points.

=== Group Deliverables ===

==== Page Design Team ====

The Page Design team is responsible for the visual appearance and internal behavior of the gene page. The core deliverable of the team is the HTML/CSS/JavaScript code for this page, in a form that can be dynamically populated based on the gene chosen by the GRNsight user. The final page design shall also design messages and alerts for errors and warnings, such as when the user attempts to display a gene page for a node that does not correspond to a ''S. cerevisiae'' gene.

The Data Analyst will complete the analysis of microarray data for the dCIN5 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

==== Gene Database APIs Team ====

The Gene Database APIs team is responsible for retrieving a gene’s data from the four APIs that have been seen in class and the assignments: UniProt, Ensembl, SGD (YeastMine), and NCBI. The core deliverable of the team is a single function, <code>getGeneInformation(geneSymbol)</code>, which receives a single gene symbol as its parameter and returns a deferred object that asynchronously delivers the gene’s data back to the caller. The gene information function shall ''transparently'' call and integrate the data from the underlying APIs without further intervention by the caller.

As the project evolves, the signature of <code>getGeneInformation</code> may change in consultation with Drs. Dahlquist and Dionisio, but its primary function should not.

The Data Analyst will complete the analysis of microarray data for the dGLN3 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

==== JASPAR API Team ====

The JASPAR API team is responsible for learning about and implementing a ''fifth'' API which has ''not'' yet been seen in class: [http://jaspar.genereg.net JASPAR], an open-access API for transcription factor binding profiles. The learning curve for both the biology and technology of this API is factored into this team, which is why it is only responsible for this one API.

The coders in the JASPAR API team will work with the coders in the Gene Database APIs team to make sure that transcription factor information is properly integrated into the <code>getGeneInformation</code> function. The Quality Assurance guild will work together to make sure that JASPAR information is effectively included in the gene page design.

The Data Analyst will complete the analysis of microarray data for the dZAP1 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

==== Interaction and Integration Team ====

The Interaction and Integration team is responsible for bringing the gene page and API code together into a cohesive and seamless whole. The team’s coders will write the “glue code” across GRNsight, the gene page, and the <code>getGeneInformation</code> function so that the gene page is correctly triggered from a displayed GRN. This includes the code that initially opens the page from GRNsight as well as the code that populates this page based on the results delivered by the <code>getGeneInformation</code> function.

The Data Analyst will complete the analysis of microarray data for the wild type dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

=== Individual Deliverable ===

The individual deliverable is an [[GRNsight Gene Page 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 Journal Entries ==

* Each team will write a combined journal entry for each week with contributions from all members.
* [[Week 11]] Creation of page, executive summaries of progress, reflections (12:01am 11/14)
* [[Week 12]] Revision of page, executive summaries of progress, reflections(12:01am 11/21)
* [[Week 14]] Executive summaries of progress, reflections (12:01am 12/5)
* [[Week 15]] Organized deliverables page (4:30pm 12/15)

== Groups ==

The project groups and roles are are:
# Page Design
#* Project Manager/Quality Assurance: Hayden
#* Data Analysis: Mary
#* Coder: Arash
#* Designer: Nicole
# Gene Database APIs
#* Project Manager/Quality Assurance: Corinne
#* Data Analysis: Dina
#* Coders: Eddie A. and John
# JASPAR API
#* Project Manager/Quality Assurance: Quinn
#* Data Analysis: Antonio
#* Coders: Eddie B. and Simon
# Interaction and Integration
#* Project Manager/Quality Assurance: Katie
#* Data Analysis: Emma
#* Coders: Blair and Zach

== 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.

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

The Quality Assurance (QA) team member is the resident expert on the gene data, ID systems, and formats. He or she should be proficient with Google Chrome Developer tools, code-savvy editors, curl, and the command line in general (as applicable) to check his or her team’s deliverable for accuracy, bugs, or any other quality-related issues. The QA is the bridge between the coders and the Data Analyst, integrating information from both parts of the team.

In many cases, the same person holds the role of Project Manager and Quality Assurance, as these two roles go together as the ones who ensure that their team’s deliverable meets the overall project’s requirements.

=== [[Data Analysis]] ===

GRNsight is a web application and service for visualizing models of gene regulatory networks. The role of the Data Analyst will be to complete the analysis of the Dahlquist Lab microarray dataset that was begun in the Week 8 and Week 10 assignments so that new insights can be gleaned by visualizing the data with GRNsight. The Data Analysts are the end-users of the software, ultimately determining if the new features are useful to them in their biological interpretation of the cold shock experiments.

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

The coder is the resident expert on the technology being used—assorted software, file management, version control, troubleshooting, programming. He or she coordinates with Drs. Dahlquist and Dionisio and fellow coders in developing the code base for the GRNsight gene page. GRNsight is written in JavaScript and is built on open source JavaScript libraries. Source code is hosted on GitHub and managed by Node.js.

== Project Milestones ==

Specific project milestones are found on the individual guild pages.

=== Guild Milestones ===

These are links to the respective milestone lists in the guild pages:
* [[Project Manager#Milestones|Project Manager]]
* [[Quality Assurance#Milestones|Quality Assurance]]
* [[Data Analysis#Milestones|Data Analysis]]
* [[Coder#Milestones|Coder]]

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

QLanners Week 14

2017-11-30T23:48:09Z

Kdahlquist: from NCBI

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database.

General info we want about each gene:
*Gene ID from each database
*Description/Function (ensembl)
*DNA Sequence (ensembl)
*Protein Sequence (UniProt)
*Locus tag (NCBI)
*Also Known As (NCBI)
*Consensus Sequence (JASPAR)
*Regulation (SGD)
*Interaction (SGD)
*Similar Proteins (UniProt)
*Gene Ontology (SGD - see if we can find it on UniProt)

We decided that from JASPAR we will pull:
*Gene ID (this will be the ''matrix id''
*Sequence Logo
*Frequency Matrix
* also get ''class'' and ''family''

Breakdown of what we want from all other databases:<br>
'''NCBI:'''
*Gene ID
*Locus Tag
*Also Known As
* Also get RefSeq IDs for chromosome, mRNA, and protein.
<br>
'''Ensembl:'''
*Gene ID
*Description/Function
*DNA Sequence
* also get chromosomal location, ''about this gene''
<br>
'''UniProt:'''
*Gene ID (Note that for UniProt, it will be a ''protein ID'', and that there are two different ones that you need to get. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:36, 30 November 2017 (PST)''
*Protein Sequence
*Similar Proteins
*Protein Type/Name
* Please get the species from UniProt as well, even though we know it is going to be yeast.
<br>
'''SGD:'''
*Gene ID
** ''Standard Name'', i.e., ''HSF1''
** ''Systematic Name'', i.e., ''YGL073W''
** ''SGD ID'', i.e., ''S000003041''
*Regulation
*Interaction
*Gene Ontology

QLanners Week 14

2017-11-30T23:47:20Z

Kdahlquist: what to get from ensembl

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database.

General info we want about each gene:
*Gene ID from each database
*Description/Function (ensembl)
*DNA Sequence (ensembl)
*Protein Sequence (UniProt)
*Locus tag (NCBI)
*Also Known As (NCBI)
*Consensus Sequence (JASPAR)
*Regulation (SGD)
*Interaction (SGD)
*Similar Proteins (UniProt)
*Gene Ontology (SGD - see if we can find it on UniProt)

We decided that from JASPAR we will pull:
*Gene ID (this will be the ''matrix id''
*Sequence Logo
*Frequency Matrix
* also get ''class'' and ''family''

Breakdown of what we want from all other databases:<br>
'''NCBI:'''
*Gene ID
*Locus Tag
*Also Known As
<br>
'''Ensembl:'''
*Gene ID
*Description/Function
*DNA Sequence
* also get chromosomal location, ''about this gene''
<br>
'''UniProt:'''
*Gene ID (Note that for UniProt, it will be a ''protein ID'', and that there are two different ones that you need to get. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:36, 30 November 2017 (PST)''
*Protein Sequence
*Similar Proteins
*Protein Type/Name
* Please get the species from UniProt as well, even though we know it is going to be yeast.
<br>
'''SGD:'''
*Gene ID
** ''Standard Name'', i.e., ''HSF1''
** ''Systematic Name'', i.e., ''YGL073W''
** ''SGD ID'', i.e., ''S000003041''
*Regulation
*Interaction
*Gene Ontology

QLanners Week 14

2017-11-30T23:46:36Z

Kdahlquist: what to get from Jaspar

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database.

General info we want about each gene:
*Gene ID from each database
*Description/Function (ensembl)
*DNA Sequence (ensembl)
*Protein Sequence (UniProt)
*Locus tag (NCBI)
*Also Known As (NCBI)
*Consensus Sequence (JASPAR)
*Regulation (SGD)
*Interaction (SGD)
*Similar Proteins (UniProt)
*Gene Ontology (SGD - see if we can find it on UniProt)

We decided that from JASPAR we will pull:
*Gene ID (this will be the ''matrix id''
*Sequence Logo
*Frequency Matrix
* also get ''class'' and ''family''

Breakdown of what we want from all other databases:<br>
'''NCBI:'''
*Gene ID
*Locus Tag
*Also Known As
<br>
'''Ensembl:'''
*Gene ID
*Description/Function
*DNA Sequence
<br>
'''UniProt:'''
*Gene ID (Note that for UniProt, it will be a ''protein ID'', and that there are two different ones that you need to get. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:36, 30 November 2017 (PST)''
*Protein Sequence
*Similar Proteins
*Protein Type/Name
* Please get the species from UniProt as well, even though we know it is going to be yeast.
<br>
'''SGD:'''
*Gene ID
** ''Standard Name'', i.e., ''HSF1''
** ''Systematic Name'', i.e., ''YGL073W''
** ''SGD ID'', i.e., ''S000003041''
*Regulation
*Interaction
*Gene Ontology

QLanners Week 14

2017-11-30T23:45:47Z

Kdahlquist: get species from UniProt

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database.

General info we want about each gene:
*Gene ID from each database
*Description/Function (ensembl)
*DNA Sequence (ensembl)
*Protein Sequence (UniProt)
*Locus tag (NCBI)
*Also Known As (NCBI)
*Consensus Sequence (JASPAR)
*Regulation (SGD)
*Interaction (SGD)
*Similar Proteins (UniProt)
*Gene Ontology (SGD - see if we can find it on UniProt)

We decided that from JASPAR we will pull:
*Gene ID
*Sequence Logo
*Frequency Matrix

Breakdown of what we want from all other databases:<br>
'''NCBI:'''
*Gene ID
*Locus Tag
*Also Known As
<br>
'''Ensembl:'''
*Gene ID
*Description/Function
*DNA Sequence
<br>
'''UniProt:'''
*Gene ID (Note that for UniProt, it will be a ''protein ID'', and that there are two different ones that you need to get. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:36, 30 November 2017 (PST)''
*Protein Sequence
*Similar Proteins
*Protein Type/Name
* Please get the species from UniProt as well, even though we know it is going to be yeast.
<br>
'''SGD:'''
*Gene ID
** ''Standard Name'', i.e., ''HSF1''
** ''Systematic Name'', i.e., ''YGL073W''
** ''SGD ID'', i.e., ''S000003041''
*Regulation
*Interaction
*Gene Ontology

QLanners Week 14

2017-11-30T23:36:46Z

Kdahlquist: note for Uniprot

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database.

General info we want about each gene:
*Gene ID from each database
*Description/Function (ensembl)
*DNA Sequence (ensembl)
*Protein Sequence (UniProt)
*Locus tag (NCBI)
*Also Known As (NCBI)
*Consensus Sequence (JASPAR)
*Regulation (SGD)
*Interaction (SGD)
*Similar Proteins (UniProt)
*Gene Ontology (SGD - see if we can find it on UniProt)

We decided that from JASPAR we will pull:
*Gene ID
*Sequence Logo
*Frequency Matrix

Breakdown of what we want from all other databases:<br>
'''NCBI:'''
*Gene ID
*Locus Tag
*Also Known As
<br>
'''Ensembl:'''
*Gene ID
*Description/Function
*DNA Sequence
<br>
'''UniProt:'''
*Gene ID (Note that for UniProt, it will be a ''protein ID'', and that there are two different ones that you need to get. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:36, 30 November 2017 (PST)''
*Protein Sequence
*Similar Proteins
*Protein Type/Name
<br>
'''SGD:'''
*Gene ID
** ''Standard Name'', i.e., ''HSF1''
** ''Systematic Name'', i.e., ''YGL073W''
** ''SGD ID'', i.e., ''S000003041''
*Regulation
*Interaction
*Gene Ontology

QLanners Week 14

2017-11-30T23:32:53Z

Kdahlquist: update SGD gene IDs

Emmatyrnauer Week 10

2017-11-30T23:03:20Z

Kdahlquist: /* Files */ link to YEASTRACT results

==Electronic Notebook==
=== Microarray Data Analysis Part 2: "High-level Analysis" ===
==== Clustering and GO Term Enrichment with stem ====
# '''Preparing the microarray data file for loading into STEM.'''
#* I downloaded my Excel workbook that I used for my [[Week 8]] assignment.
#* I inserted a new worksheet into my Excel workbook and named it "wt_stem".
#* I selected all of the data from my "wt_ANOVA" worksheet and Pasted special > paste values into my "wt_stem" worksheet.
#** I made sure that the leftmost column had the column header "Master_Index" and renamed this column to "SPOT". I made sure Column B was named "ID"and renamed this column to "Gene Symbol". I deleted the column named "Standard_Name".
#** I filtered the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data was filtered, I selected all of the rows (except for the header row) and deleted the rows by right-clicking and choosing "Delete Row" from the context menu. I then undid the filter. This ensured that only the genes with a "significant" change in expression, and not the noise, would be clustered. <span style="color:red">1822 genes were left </span>
#** I then deleted all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** I renamed the data columns with just the time and units (for example, 15m, 30m, etc.).
#** I saved my work and used ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt), clicked OK to the warnings and closed the file. ("wt_stem.txt" located in the compressed file: "Week10_filesforstem_wildtype_emmat.zip‎")
#*** I made sure all of the file extensions were turned on.
# '''I downloaded and extracted the STEM software from [http://www.cs.cmu.edu/~jernst/stem/ here].'''
#* I clicked on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], registered, and downloaded the <code>stem.zip</code> file to the Desktop.
#* I unziped the file.
#* This created a folder called <code>stem</code>. Inside the folder, I double-clicked on the <code>stem.jar</code> to launch the STEM program.
# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, I clicked on the ''Browse...'' button to navigate to and select my file.
##* I clicked on the radio button ''No normalization/add 0''.
##* I checked the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, I selected ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. I selected ''No cross references'', from the Cross Reference Source drop-down menu. I selected ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, I made sure that the Clustering Method said "STEM Clustering Method" and did not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) I clicked on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window opened called "All STEM Profiles (1)". Each box corresponded to a model expression profile. Colored profiles had a statistically significant number of genes assigned; they were arranged in order from most to least significant p value. Profiles with the same color belonged to the same cluster of profiles. The number in each box was simply an ID number for the profile.
##* I clicked on the button that said "Interface Options...". At the bottom of the Interface Options window that appeared below where it said "X-axis scale should be:", I clicked on the radio button that said "Based on real time," then closed the Interface Options window.
##*I took a screenshot of this window and pasted it into a PowerPoint presentation to save my figures.
## I clicked on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* I took a screenshot of each of the individual profile windows and saved the images in my PowerPoint presentation (Wt_profileimage_presentation_emmat.pptx)
##* At the bottom of each profile window, there were two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, I clicked on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appeared, I clicked on the "Save Table" button and saved the file to the desktop. I made sure the filename was descriptive of the contents: wt_profile#_genelist.txt
##** I compressed and uploaded these files to the wiki and linked to them on my individual journal page. ("wt_profilenumber_genelist_emmat" located in compressed file: "Week10_filesforstem_wildtype_emmat.zip‎")
##* For each of the significant profiles, I clicked on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appeared, I clicked on the "Save Table" button and saved the file to the desktop. I made the filename descriptive of the contents: wt_profile#_GOlist.txt. At this point I had saved all of the primary data from the STEM software and began interpretation of the results.
##** I compressed and uploaded these files to the wiki and linked to them on my individual journal page. ("wt_profilenumber_GOlist_emmat" located in compressed file: "Week10_filesforstem_wildtype_emmat.zip‎")
# '''Analyzing and Interpreting STEM Results'''
## I selected one of the profiles I saved in the previous step for further interpretation of the data.
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##**<span style="color:red">I chose profile 45 because it shows a general trend of up regulation of genes at the cold shock time point.</span>
##* '''''How many genes belong to this profile?'''''
##**<span style="color:red">549 genes belong to this profile.</span>
##* '''''How many genes were expected to belong to this profile?'''''
##**<span style="color:red">47.1 genes were expected to belong to this profile.</span>
##* '''''What is the p value for the enrichment of genes in this profile?''''' (This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.)
##**<span style="color:red">0.00 is the p-value for the enrichment of genes in this profile.</span>
##* I opened the GO list file I saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. I selected the third row and then chose from the menu Data > Filter > Autofilter. I filtered on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' <span style="color:red">240 GO terms are associated with profile 45 at p<0.05. </span> The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. I filtered on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?''''' <span style="color:red">39 GO terms are associated with profile 45 with a corrected p value < 0.05.</span>
##* I selected 6 Gene Ontology terms from my filtered list of corrected p < 0.05.
##**'''''I looked up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In my final presentation, I will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor being deleted (for the Δgln3 and Δswi4 groups)?'''''
##** To look up the definitions, I went to [http://geneontology.org http://geneontology.org].
##** I copied and pasted the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, I clicked on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition was on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].
##***<span style="color:red">'''ribosome assembly''' (GO:0042255): The aggregation, arrangement and bonding together of the mature ribosome and of its subunits</span> [http://amigo.geneontology.org/amigo/term/GO:0042255]
##***<span style="color:red">'''RNA modification''' (GO:0009451): The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically</span> [http://amigo.geneontology.org/amigo/term/GO:0009451]
##***<span style="color:red">'''ncRNA catabolic process''' (GO:0034661): The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts</span> [http://amigo.geneontology.org/amigo/term/GO:0034661]
##***<span style="color:red">'''intracellular membrane-bounded organelle''' (GO:0043231): Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane</span> [http://amigo.geneontology.org/amigo/term/GO:0043231]
##***<span style="color:red">'''nucleoplasm''' (GO:0005654): That part of the nuclear content other than the chromosomes or the nucleolus.</span> [http://amigo.geneontology.org/amigo/term/GO:0005654]
##***<span style="color:red">'''ribosomal subunit export from nucleus''' (GO:0000054): The directed movement of a ribosomal subunit from the nucleus into the cytoplasm. </span> [http://amigo.geneontology.org/amigo/term/GO:0000054]
##**** '''Why does the cell react to cold shock by changing the expression of genes associated with these GO terms?''' The activity of these genes associated with these GO terms may increase to maintain viability of the cell in a highly-stressed environment. Furthermore, these genes may increase in expression to allow for greater efficiency of the cell during harsh conditions so that unnecessary energy is not expended.
====Files====
#Updated excel spreadsheet: [[Media:Wt_Microarraydata_ET.zip]]
#Updated powerpoint presentation: [[Media:Wt_profileimage_presentation_emmat.pptx]]
#File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
#YEASTRACT rank by TF results: [[Media:YEASTRACT_results_ET_20171130.xlsx | YEASTRACT_results_ET_20171130.xlsx]]

====Conclusion====
For the assignment this week, we did clustering and GO term enrichment with STEM, downloaded and ran the STEM software using an updated excel spreadsheet, obtained figures and results from the software, and analyzed and interpreted the STEM results. A new worksheet was created in the excel workbook from week 8 that involved renaming and filtering data from the wt_ANOVA worksheet. Using this updated file, STEM created figures and tables representing clusters/profiles of genes with similar responses in terms of expression following cold shock. One profile was chosen (45) for further analysis in terms of the identification of genes associated with different p-values within the profile, and 6 GO terms were selected from the filtered list of corrected p<0.05 and looked up with http://geneontology.org. Based on the GO terms that were designated for each cluster, I hypothesize that genes which code for parts of the cell which are needed for cell survival/cell rescue will be upregulated. On the other hand, genes involved in processes that aren't required for cell survival may be downregulated to conserve energy.

==Acknowledgements==
#I worked with my homework partner [[User:cazinge|Eddie Azinge]] during class and over text.
#Dr. Dahlquist for teaching and assisting us with the data analysis
# I copied and modified the instructions from the [[Week 10]] assignment page.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 15:14, 31 October 2017 (PDT)

==References==
#Gene Ontology Consortium. (2017). The Gene Ontology. Retrieved November 19, 2017, from http://geneontology.org
#*Ribosome assembly. The Gene Ontology. Retrieved November 19, 2017, from http://amigo.geneontology.org/amigo/term/GO:0042255
#*RNA modification. The Gene Ontology. Retrieved November 19, 2017, from http://amigo.geneontology.org/amigo/term/GO:0009451
#*ncRNA catabolic process. The Gene Ontology. Retrieved November 19, 2017, from http://amigo.geneontology.org/amigo/term/GO:0034661
#* Nucleoplasm. The Gene Ontology. Retrieved November 19, 2017, from http://amigo.geneontology.org/amigo/term/GO:0005654
#*Intracellular membrane-bounded organelle. The Gene Ontology. Retrieved November 19, 2017, http://amigo.geneontology.org/amigo/term/GO:0043231
#*Ribosomal subunit export from nucleus. The Gene Ontology. Retrieved November 19, 2017, from http://amigo.geneontology.org/amigo/term/GO:0000054
#LMU BioDB 2017. (2017). Week 10. Retrieved November 19, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#Short Time-series Expression Miner (STEM). (2006). Retrieved November 19, 2017, from http://www.cs.cmu.edu/~jernst/stem/
{{Emmatyrnauer}}

File:YEASTRACT results ET 20171130.xlsx

2017-11-30T23:02:24Z

Kdahlquist: YEASTRACT results for Emma

YEASTRACT results for Emma

GRNsight Gene Page Project

2017-11-30T22:01:28Z

Kdahlquist: /* Project Milestones */ commented out the overall flow section because never filled in

{{GRNsight Gene Page Project Links}}

== Overall Project Goal ==

The GRNsight gene page project seeks to add significant functionality to GRNsight by allowing users to open a gene information page from a chosen gene in the currently displayed ''Saccharomyces cerevisiae'' gene regulation network. The gene information page shall open a new browser tab or window and display, in an informative and visually effective way, the information known about this gene based on five APIs: UniProt, Ensembl, SGD (YeastMine), NCBI, and JASPAR.

For this project, we shall restrict the current organism to just ''Saccharomyces cerevisiae''. Because GRNsight can be used to display GRNs from any species—and in fact to display graphs that are not GRNs at all—the gene page functionality shall be robust enough to handle non-''S. cerevisiae'' nodes in a graceful and informative manner.

To facilitate the development of the gene page, the class has been divided into four groups:
* Page Design
* Gene Database APIs
* JASPAR API
* Interaction and Integration

Each team is responsible for a specific portion of the overall gene page, detailed below. The members of each team will also have specific roles, also detailed below. Team members in a specific role are also expected to work with each other across teams as ''guilds'', in order to keep each component of the project coordinated and consistent.

== Common Deliverables ==

* You will give a final group [[GRNsight Gene Page Project Deliverables#PowerPoint_Presentation | PowerPoint presentation]] in class during the final exam period on '''Tuesday, December 12, 2:00pm'''.
* Final due date for all other deliverables is no later than '''Friday, December 15, 4:30pm''' (according to official final exam schedule for fall, 2017).
* 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 [[GRNsight Gene Page Project Deliverables#Group Report|group report]] and [[GRNsight Gene Page Project Deliverables#Individual Assessment and Reflection|individual assessment and reflection]], are given on the [[GRNsight Gene Page Project Deliverables]] page.

=== Group Deliverables ===

==== Page Design Team ====

The Page Design team is responsible for the visual appearance and internal behavior of the gene page. The core deliverable of the team is the HTML/CSS/JavaScript code for this page, in a form that can be dynamically populated based on the gene chosen by the GRNsight user. The final page design shall also design messages and alerts for errors and warnings, such as when the user attempts to display a gene page for a node that does not correspond to a ''S. cerevisiae'' gene.

The Data Analyst will complete the analysis of microarray data for the dCIN5 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

==== Gene Database APIs Team ====

The Gene Database APIs team is responsible for retrieving a gene’s data from the four APIs that have been seen in class and the assignments: UniProt, Ensembl, SGD (YeastMine), and NCBI. The core deliverable of the team is a single function, <code>getGeneInformation(geneSymbol)</code>, which receives a single gene symbol as its parameter and returns a deferred object that asynchronously delivers the gene’s data back to the caller. The gene information function shall ''transparently'' call and integrate the data from the underlying APIs without further intervention by the caller.

As the project evolves, the signature of <code>getGeneInformation</code> may change in consultation with Drs. Dahlquist and Dionisio, but its primary function should not.

The Data Analyst will complete the analysis of microarray data for the dGLN3 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

==== JASPAR API Team ====

The JASPAR API team is responsible for learning about and implementing a ''fifth'' API which has ''not'' yet been seen in class: [http://jaspar.genereg.net JASPAR], an open-access API for transcription factor binding profiles. The learning curve for both the biology and technology of this API is factored into this team, which is why it is only responsible for this one API.

The coders in the JASPAR API team will work with the coders in the Gene Database APIs team to make sure that transcription factor information is properly integrated into the <code>getGeneInformation</code> function. The Quality Assurance guild will work together to make sure that JASPAR information is effectively included in the gene page design.

The Data Analyst will complete the analysis of microarray data for the dZAP1 dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

==== Interaction and Integration Team ====

The Interaction and Integration team is responsible for bringing the gene page and API code together into a cohesive and seamless whole. The team’s coders will write the “glue code” across GRNsight, the gene page, and the <code>getGeneInformation</code> function so that the gene page is correctly triggered from a displayed GRN. This includes the code that initially opens the page from GRNsight as well as the code that populates this page based on the results delivered by the <code>getGeneInformation</code> function.

The Data Analyst will complete the analysis of microarray data for the wild type dataset, visualizing the final gene regulatory network in GRNsight and reporting on the usability of the new feature.

=== Individual Deliverable ===

The individual deliverable is an [[GRNsight Gene Page 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 Journal Entries ==

* Each team will write a combined journal entry for each week with contributions from all members.
* [[Week 11]] Creation of page, executive summaries of progress, reflections (12:01am 11/14)
* [[Week 12]] Revision of page, executive summaries of progress, reflections(12:01am 11/21)
* [[Week 14]] Executive summaries of progress, reflections (12:01am 12/5)
* [[Week 15]] Organized deliverables page (4:30pm 12/15)

== Groups ==

The project groups and roles are are:
# Page Design
#* Project Manager/Quality Assurance: Hayden
#* Data Analysis: Mary
#* Coder: Arash
#* Designer: Nicole
# Gene Database APIs
#* Project Manager/Quality Assurance: Corinne
#* Data Analysis: Dina
#* Coders: Eddie A. and John
# JASPAR API
#* Project Manager/Quality Assurance: Quinn
#* Data Analysis: Antonio
#* Coders: Eddie B. and Simon
# Interaction and Integration
#* Project Manager/Quality Assurance: Katie
#* Data Analysis: Emma
#* Coders: Blair and Zach

== 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.

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

The Quality Assurance (QA) team member is the resident expert on the gene data, ID systems, and formats. He or she should be proficient with Google Chrome Developer tools, code-savvy editors, curl, and the command line in general (as applicable) to check his or her team’s deliverable for accuracy, bugs, or any other quality-related issues. The QA is the bridge between the coders and the Data Analyst, integrating information from both parts of the team.

In many cases, the same person holds the role of Project Manager and Quality Assurance, as these two roles go together as the ones who ensure that their team’s deliverable meets the overall project’s requirements.

=== [[Data Analysis]] ===

GRNsight is a web application and service for visualizing models of gene regulatory networks. The role of the Data Analyst will be to complete the analysis of the Dahlquist Lab microarray dataset that was begun in the Week 8 and Week 10 assignments so that new insights can be gleaned by visualizing the data with GRNsight. The Data Analysts are the end-users of the software, ultimately determining if the new features are useful to them in their biological interpretation of the cold shock experiments.

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

The coder is the resident expert on the technology being used—assorted software, file management, version control, troubleshooting, programming. He or she coordinates with Drs. Dahlquist and Dionisio and fellow coders in developing the code base for the GRNsight gene page. GRNsight is written in JavaScript and is built on open source JavaScript libraries. Source code is hosted on GitHub and managed by Node.js.

== Project Milestones ==

Specific project milestones are found on the individual guild pages.

=== Guild Milestones ===

These are links to the respective milestone lists in the guild pages:
* [[Project Manager#Milestones|Project Manager]]
* [[Quality Assurance#Milestones|Quality Assurance]]
* [[Data Analysis#Milestones|Data Analysis]]
* [[Coder#Milestones|Coder]]

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

GRNsight Gene Page Project Deliverables

2017-11-30T22:00:01Z

Kdahlquist: /* Deliverables Checklist */ put in grading

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

=== Grading ===

* The Group Report is worth 50 points.
* The Group PowerPoint presentation is worth 50 points.
* All other deliverables listed above, together, are worth 50 points.

== 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. 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 and should be 3-5 pages long (double-spaced). 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
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page 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 GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== 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.

Create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text. You should provide citations to the individual electronic notebooks of the team members as appropriate in the text so that the reader knows where to go for additional details.

=== 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.

==== Results of Microarray Data Analysis ====

* Table of ANOVA results from the [[Week 8]], discussing the interpretation of the p values.
* From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the [[Week 10]] journal assignment.
** Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
** Discuss what the p values for the cluster and for the GO term list mean.
** Discuss the biological interpretation of your GO terms.
* Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
** Describe how and why you and your partner chose these transcription factors for your network.
** Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
* Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
* Interpret the results of the model as visualized in GRNsight.

==== Coding Results ====

* Give a narrative description of the new features created by the Coders.
** Provide code snippets and/or screenshots to illustrate as necessary.

=== Discussion ===

* Overall, what have you learned about the regulation of cold shock in yeast?
* How does the new feature facilitate the data analysis?
* Relate the results of your project to the papers you presented for journal club in [[Week 11]] (Coders) and [[Week 12]] (Data Analyst/QA).
** Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* 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_Fall2017_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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== 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 12 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:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be 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.

== 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 your team’s portion of the GRNsight Gene Page 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?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

Main Page

2017-11-30T21:58:20Z

Kdahlquist: /* Upcoming Seminars */ removed old seminar

__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 2017</div>

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

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 3'''
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium

=== Undergraduate Library Research Award ===

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

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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Main Page

2017-11-29T17:28:53Z

Kdahlquist: /* Upcoming Seminars */ delete second candidate

__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 2017</div>

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

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 3'''
** '''Model Lesson on Animal Physiology:''' Thursday, 11/30 at 11:30 AM, PER 200
** '''Lunch with Students:''' Thursday, 11/30, 12:30-1:30, LSB 2nd floor Terrace
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium

=== Undergraduate Library Research Award ===

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

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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Main Page

2017-11-28T18:16:35Z

Kdahlquist: /* Announcements */ uncomment undergraduate library research award

__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 2017</div>

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

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 2'''
** '''Model Lesson on Animal Physiology:''' Monday, 11/27 at 10:20 AM, LSB 116
** '''Research Seminar:''' Tuesday, 11/28 at 11:30 AM, LSB auditorium
** '''Lunch with Students:''' Tuesday, 11/28 at 12:30-1:30, LSB 2nd floor Terrace
* '''Biology Faculty Candidate 3'''
** '''Model Lesson on Animal Physiology:''' Thursday, 11/30 at 11:30 AM, PER 200
** '''Lunch with Students:''' Thursday, 11/30, 12:30-1:30, LSB 2nd floor Terrace
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium

=== Undergraduate Library Research Award ===

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

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

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Main Page

2017-11-28T18:15:13Z

Kdahlquist: /* Upcoming Seminars */ delete candidate 1

__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 2017</div>

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

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 2'''
** '''Model Lesson on Animal Physiology:''' Monday, 11/27 at 10:20 AM, LSB 116
** '''Research Seminar:''' Tuesday, 11/28 at 11:30 AM, LSB auditorium
** '''Lunch with Students:''' Tuesday, 11/28 at 12:30-1:30, LSB 2nd floor Terrace
* '''Biology Faculty Candidate 3'''
** '''Model Lesson on Animal Physiology:''' Thursday, 11/30 at 11:30 AM, PER 200
** '''Lunch with Students:''' Thursday, 11/30, 12:30-1:30, LSB 2nd floor Terrace
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium


== 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:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Template:Pagedesiigner

2017-11-21T21:41:39Z

Kdahlquist: replaced links table with template so that changes show up appropriately on their page (noticed outdated link)

[[Category:Page Desiigner]]
[[Category:Group Projects]]

{{ GRNsight Gene Page Project Links }}

===Page Desiigner Schedule===
[[Page Desiigner Schedule]]

===Uploaded Files===
[[File:Data Driven Design.zip]]
<br>
[[Media:MaryHaydenWeek12JournalClubPresentation.pptx ‎]]
===Individual Contributer Pages===
[[User:ArashLari|Arash Lari]]
<br>
[[User:hhinsch|Hayden Hinsch]]
<br>
[[User:Mbalducc|Mary Balducci]]
<br>
[[User:Nicolekalcic|Nicole Kalcic]]

Main Page

2017-11-21T21:40:09Z

Kdahlquist: deleted old comment

__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 2017</div>

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

== Announcements ==

* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 1'''
** '''Model Physiology Class:''' Monday, November 20, 10:20 AM, LSB 116.
** '''Research Seminar:''' Tuesday, November 21, 11:30 AM, LSB Auditorium.
** '''Lunch with Students:''' Tuesday, November 22, 12:30-1:30, LSB 2nd Floor Terrace.
* '''Biology Faculty Candidate 2'''
** '''Model Lesson on Animal Physiology:''' Monday, 11/27 at 10:20 AM, LSB 116
** '''Research Seminar:''' Tuesday, 11/28 at 11:30 AM, LSB auditorium
** '''Lunch with Students:''' Tuesday, 11/28 at 12:30-1:30, LSB 2nd floor Terrace
* '''Biology Faculty Candidate 3'''
** '''Model Lesson on Animal Physiology:''' Thursday, 11/30 at 11:30 AM, PER 200
** '''Lunch with Students:''' Thursday, 11/30, 12:30-1:30, LSB 2nd floor Terrace
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium


== 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:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Week 15

2017-11-21T01:08:10Z

Kdahlquist: add period

'''The Group PowerPoint presentation is due Tuesday, December 12, at 12:01 am PST.'''

'''The final journal entry is due on Friday, December 15, at 4:30 pm PST.'''

== Overview ==

The purpose of this assignment is to complete the team projects as noted on the [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] page.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] for this week in an '''''electronic lab 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 or flash drive) by the final deadline of Friday, December 15, 4:30 PM.

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

Week 15

2017-11-21T01:07:48Z

Kdahlquist: line break between due dates; link to deliverables

'''The Group PowerPoint presentation is due Tuesday, December 12, at 12:01 am PST'''

'''The final journal entry is due on Friday, December 15, at 4:30 pm PST.'''

== Overview ==

The purpose of this assignment is to complete the team projects as noted on the [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] page.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] for this week in an '''''electronic lab 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 or flash drive) by the final deadline of Friday, December 15, 4:30 PM.

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

Week 15

2017-11-21T01:06:25Z

Kdahlquist: stubbed out assignment

'''The Group PowerPoint presentation is due Tuesday, December 12, at 12:01 am PST'''
'''The final journal entry is due on Friday, December 15, at 4:30 pm PST.'''

== Overview ==

The purpose of this assignment is to complete the team projects.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] for this week in an '''''electronic lab 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 or flash drive) by the final deadline of Friday, December 15, 4:30 PM.

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

Week 14

2017-11-21T01:01:40Z

Kdahlquist: /* Overview */ link to deliverables page

'''This journal entry is due on Tuesday, December 5, at 12:01 PDT.''' ''(Monday night/Tuesday morning)''

== Overview ==

The objectives of this week's exercise is to make significant progress toward completing the group project [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] according to the schedule set by your group.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 3 points.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] for this week in an '''''electronic lab notebook'''''.

== '''Team Journal Assignment''' ==

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# 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]]

Week 14

2017-11-21T01:01:06Z

Kdahlquist: /* Electronic Lab Notebook */ link to deliverables page

'''This journal entry is due on Tuesday, December 5, at 12:01 PDT.''' ''(Monday night/Tuesday morning)''

== Overview ==

The objectives of this week's exercise is to make significant progress toward completing the group project deliverables according to the schedule set by your group.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 3 points.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[GRNsight_Gene_Page_Project_Deliverables | deliverables]] for this week in an '''''electronic lab notebook'''''.

== '''Team Journal Assignment''' ==

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# 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]]

Week 14

2017-11-21T01:00:10Z

Kdahlquist: /* Team Membership */ changed to electronic lab notebook.

'''This journal entry is due on Tuesday, December 5, at 12:01 PDT.''' ''(Monday night/Tuesday morning)''

== Overview ==

The objectives of this week's exercise is to make significant progress toward completing the group project deliverables according to the schedule set by your group.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 3 points.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress for this week in an '''''electronic lab notebook'''''.

== '''Team Journal Assignment''' ==

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# 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]]

Week 14

2017-11-21T00:59:06Z

Kdahlquist: /* Overview */ noted group schedule

'''This journal entry is due on Tuesday, December 5, at 12:01 PDT.''' ''(Monday night/Tuesday morning)''

== Overview ==

The objectives of this week's exercise is to make significant progress toward completing the group project deliverables according to the schedule set by your group.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 3 points.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Team Membership ===

The project groups and roles are are:
# Page Design
#* Project Manager/Quality Assurance: Hayden
#* Data Analysis: Mary
#* Coder: Arash
#* Designer: Nicole
# Gene Database APIs
#* Project Manager/Quality Assurance: Corinne
#* Data Analysis: Dina
#* Coders: Eddie A. and John
# JASPAR API
#* Project Manager/Quality Assurance: Quinn
#* Data Analysis: Antonio
#* Coders: Eddie B. and Simon
# Interaction and Integration
#* Project Manager/Quality Assurance: Katie
#* Data Analysis: Emma
#* Coders: Blair and Zach

== '''Team Journal Assignment''' ==

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# 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]]

Week 14

2017-11-21T00:58:33Z

Kdahlquist: stubbed out assignment

'''This journal entry is due on Tuesday, December 5, at 12:01 PDT.''' ''(Monday night/Tuesday morning)''

== Overview ==

The objectives of this week's exercise is to make significant progress toward completing the group project deliverables.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 3 points.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual progress in your '''''electronic laboratory notebook'''''.

=== Team Membership ===

The project groups and roles are are:
# Page Design
#* Project Manager/Quality Assurance: Hayden
#* Data Analysis: Mary
#* Coder: Arash
#* Designer: Nicole
# Gene Database APIs
#* Project Manager/Quality Assurance: Corinne
#* Data Analysis: Dina
#* Coders: Eddie A. and John
# JASPAR API
#* Project Manager/Quality Assurance: Quinn
#* Data Analysis: Antonio
#* Coders: Eddie B. and Simon
# Interaction and Integration
#* Project Manager/Quality Assurance: Katie
#* Data Analysis: Emma
#* Coders: Blair and Zach

== '''Team Journal Assignment''' ==

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# 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]]

Main Page

2017-11-21T00:54:17Z

Kdahlquist: /* Announcements */ modified announcement

__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 2017</div>

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

== Announcements ==

* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 1'''
** '''Model Physiology Class:''' Monday, November 20, 10:20 AM, LSB 116.
** '''Research Seminar:''' Tuesday, November 21, 11:30 AM, LSB Auditorium.
** '''Lunch with Students:''' Tuesday, November 22, 12:30-1:30, LSB 2nd Floor Terrace.
* '''Biology Faculty Candidate 2'''
** '''Model Lesson on Animal Physiology:''' Monday, 11/27 at 10:20 AM, LSB 116
** '''Research Seminar:''' Tuesday, 11/28 at 11:30 AM, LSB auditorium
** '''Lunch with Students:''' Tuesday, 11/28 at 12:30-1:30, LSB 2nd floor Terrace
* '''Biology Faculty Candidate 3'''
** '''Model Lesson on Animal Physiology:''' Thursday, 11/30 at 11:30 AM, PER 200
** '''Lunch with Students:''' Thursday, 11/30, 12:30-1:30, LSB 2nd floor Terrace
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium



== 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:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page 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 12:01am. 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 Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[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)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* 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]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [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.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[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://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [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://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

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

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[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 [http://brightspace.lmu.edu on Brightspace])

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

| Introduction to DNA microarray data
* Experimental design
* [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]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

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

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

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

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| 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/>12/15/2017 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:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''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 web, 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 1. The withdrawal or credit/no-credit status deadline is November 3.

=== 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/wellness/lmucares/aboutlmucares/livethelionscode/ 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 and other ancillary 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, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.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/fall2017/. You will need to have a user account on this wiki 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 the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email 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 email 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 [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* 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
* Account for this wiki
* [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 [http://brightspace.lmu.edu Brightspace].

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. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

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 12:01am on Tuesday Pacific time; 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.
* 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).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== 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 ====



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 will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. 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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== 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 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/fall2017/.

Data Analysis

2017-11-21T00:52:47Z

Kdahlquist: /* Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight */ added links to week 10 instructions

{{GRNsight Gene Page Project Links}}

GRNsight is a web application and service for visualizing models of gene regulatory networks. The role of the Data Analyst will be to complete the analysis of the Dahlquist Lab microarray dataset that was begun in the [[Week 8]] and [[Week 10]] assignments so that new insights can be gleaned by visualizing the data with GRNsight. The Data Analysts are the end-users of the software, ultimately determining if the new features are useful to them in their biological interpretation of the cold shock experiments.

== Guild Members ==

* Page Design: Mary (dCIN5 dataset)
* Gene Database APIs: Dina (dGLN3 dataset)
* JASPAR API: Antonio (dZAP1 dataset)
* Interaction and Integration: Emma (wild type dataset)

== Milestones ==

The milestones do not necessarily correspond to particular weeks; instead they are sets of tasks grouped together.

=== Milestone 1: Annotated Bibliography ===

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

=== Milestone 2: Journal Club Presentation ===

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

=== Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight ===

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

Week 10

2017-11-21T00:50:42Z

Kdahlquist: /* Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes */ raised level of header

'''This journal entry is due on Tuesday, November 7, at 12:01 AM PDT.'''

== Objectives ==

The purpose of this assignment is:
* to perform "high level" analysis on microarray data in preparation for the final research project.

== 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).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week, the electronic laboratory notebook you will keep on your individual wiki page is crucial. 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.
** We will be building upon the [[Week 8]] microarray data analsyis, performing additional "high level" analyses. In the interests of reproducible research, it is appropriate to copy and paste the methods from this assignment into your individual journal entry.
** You '''''must''''' then '''''modify''''' the general instructions (which are generic to the whole class) to your own data analysis, recording the specific modifications and equations that you used on '''your''' dataset.
** Record the answers to the questions posed in the protocol at the place in which they appear in the method. You do not need to separate them out in a different results section.
** All files generated in the protocol must be uploaded to the wiki and linked to from your journal entry page.
** You will write a summary paragraph that gives the conclusions from this week's analysis.

=== Homework Partners ===

Homework partners for this week are listed below. The particular dataset that you and your partner will work on is also indicated below. You are expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). You must give the details of the interaction with your partner in the [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment. Since this week's work is a continuation of the microarray data analysis you performed for the [[Week 8]] assignment, you will return to those homework partners.
* Eddie Azinge, Emma Tyrnauer: wild type data
* Eddie Bachoura, Quinn Lanners: dASH1 data
* Mary Balducci, Simon Wroblewski: dCIN5 data
* Dina Bashoura, Zach Van Ysseldyk: dGLN3 data
* Blair Hamilton, Nicole Kalcic: dHAP4 data
* Hayden Hinsch, Arash Lari: dHMO1 data
* John Lopez, Corinne Wong: dSWI4 data
* Antonio Porras, Katie Wright: dZAP1 data

=== Microarray Data Analysis Part 2: "High-level Analysis" ===

We will be working on the protocols in class on Tuesday, October 31 and Thursday, November 2. Whatever you do not finish in class will be homework to be completed by the Week 10 journal deadline.

==== Background ====

This is a list of steps required to analyze DNA microarray data.

#Quantitate the fluorescence signal in each spot
#Calculate the ratio of red/green fluorescence
#Log<sub>2</sub> transform the ratios
#* Steps 1-3 have been performed for you by the GenePix Pro software (which runs the microarray scanner).
#Normalize the ratios on each microarray slide
#Normalize the ratios for a set of slides in an experiment
#* Steps 4-5 was performed for you using a script in R, a statistics package (see: [https://openwetware.org/wiki/Dahlquist:Microarray_Data_Analysis_Workflow#Steps_4-5:_Within-_and_Between-chip_Normalization Microarray Data Analysis Workflow])
#* You will perform the following steps:
#Perform statistical analysis on the ratios
#Compare individual genes with known data
#* Steps 6-7 are performed in Microsoft Excel
#Pattern finding algorithms (clustering)
#Map onto biological pathways
#* We will use software called STEM for the clustering and mapping
# Identifying regulatory transcription factors responsible for observed changes in gene expression
# Dynamical systems modeling of the gene regulatory network ([http://kdahlquist.github.io/GRNmap/ GRNmap])
# Viewing modeling results in [http://dondi.github.io/GRNsight/ GRNsight]

==== Clustering and GO Term Enrichment with stem ====

# '''Prepare your microarray data file for loading into STEM.'''
#* Download your Excel workbook that you used for your [[Week 8]] assignment.
#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
#* Select all of the data from your "(STRAIN)_ANOVA" worksheet and Paste special > paste values into your "(STRAIN)_stem" worksheet.
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise. '''''Record the number of genes left in your electronic notebook.'''''
#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
#** Save your work. Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
#*** Note that you should turn on the file extensions if you have not already done so.
# '''Now download and extract the STEM software.''' [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
#* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
#* Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
#* This will create a folder called <code>stem</code>. Inside the folder, double-click on the <code>stem.jar</code> to launch the STEM program.

# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
##* Click on the radio button ''No normalization/add 0''.
##* Check the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, select ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. Select ''No cross references'', from the Cross Reference Source drop-down menu. Select ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) click on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
##* Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
##*Take a screenshot of this window (on a PC, simultaneously press the <code>Alt</code> and <code>PrintScreen</code> buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.
## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
# '''Analyzing and Interpreting STEM Results'''
## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following:
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##* '''''How many genes belong to this profile?'''''
##* '''''How many genes were expected to belong to this profile?'''''
##* '''''What is the p value for the enrichment of genes in this profile?''''' Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
##* Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
##** Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor that was deleted from your strain?'''''
##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].

'''''This is the stopping point for the Week 10 Assignment.''''' We will pick up the next steps in the analysis in subsequent weeks.

=== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ===

In the previous analysis using STEM, we found a number of gene expression profiles (aka clusters) which grouped genes based on similarity of gene expression changes over time. The implication is that these genes share the same expression pattern because they are regulated by the same (or the same set) of transcription factors. We will explore this using the YEASTRACT database.

# Open the gene list in Excel for the one of the significant profiles from your stem analysis. Choose a cluster with a clear cold shock/recovery up/down or down/up pattern. You should also choose one of the largest clusters.
#* Copy the list of gene IDs onto your clipboard.
# Launch a web browser and go to the [http://www.yeastract.com/ YEASTRACT database].
#* On the left panel of the window, click on the link to [http://www.yeastract.com/formrankbytf.php ''Rank by TF''].
#* Paste your list of genes from your cluster into the box labeled ''ORFs/Genes''.
#* Check the box for ''Check for all TFs''.
#* Accept the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
#* Do '''''not''''' apply a filter for "Filter Documented Regulations by environmental condition".
#* Rank genes by TF using: The % of genes in the list and in YEASTRACT regulated by each TF.
#* Click the ''Search'' button.
# Answer the following questions:
#* In the results window that appears, the p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant". '''''How many transcription factors are green or "significant"?'''''
#* '''''Copy the table of results from the web page and paste it into a new Excel workbook to preserve the results.'''''
#** '''''Upload the Excel file to OWW or Box and link to it in your electronic lab notebook.'''''
#** '''''Is your transcription factor on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".''''' (Note that this doesn't apply to the wt strain).
# For the mathematical model and GRNsight, we need to define a ''gene regulatory network'' of transcription factors that regulate other transcription factors. We can use YEASTRACT to assist us with creating the network. We want to generate a network with approximately 15-30 transcription factors in it.
#* You need to select from this list of "significant" transcription factors, which ones you will use to run the model. You will use these transcription factors and add GLN3 and HAP4 if they are not in your list. Explain in your electronic notebook how you decided on which transcription factors to include. Record the list and your justification in your electronic lab notebook.
#* Go back to the YEASTRACT database and follow the link to ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]''.
#* Copy and paste the list of transcription factors you identified (plus the transcription factor deleted in your strain) into both the "Transcription factors" field and the "Target ORF/Genes" field.
#* We are going to use the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence"
#** Click the "Generate" button.
#** In the results window that appears, click on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appears and save it to your Desktop. Rename this file with a meaningful name so that you can distinguish it from the other files you will generate.



=== Visualizing Your Gene Regulatory Networks with GRNsight===

We will analyze the regulatory matrix files you generated above in Microsoft Excel and visualize them using GRNsight to determine which one will be appropriate to pursue further in the modeling.
# First we need to properly format the output files from YEASTRACT. You will repeat these steps for each of the three files you generated above.
#* Open the file in Excel. It will not open properly in Excel because a semicolon was used as the column delimiter instead of a comma. To fix this, Select the entire Column A. Then go to the "Data" tab and select "Text to columns". In the Wizard that appears, select "Delimited" and click "Next". In the next window, select "Semicolon", and click "Next". In the next window, leave the data format at "General", and click "Finish". This should now look like a table with the names of the transcription factors across the top and down the first column and all of the zeros and ones distributed throughout the rows and columns. This is called an "adjacency matrix." If there is a "1" in the cell, that means there is a connection between the trancription factor in that row with that column.
#* Save this file in Microsoft Excel workbook format (.xlsx).
#* Check to see that all of the transcription factors in the matrix are connected to at least one of the other transcription factors by making sure that there is at least one "1" in a row or column for that transcription factor. If a factor is not connected to any other factor, delete its row and column from the matrix. Make sure that you still have somewhere between 15 and 30 transcription factors in your network after this pruning.
#** Only delete the transcription factor if there are all zeros in its column '''AND''' all zeros in its row. You may find visualizing the matrix in GRNsight (below) can help you find these easily.
#* For this adjacency matrix to be usable in GRNmap (the modeling software) and GRNsight (the visualization software), we need to transpose the matrix. Insert a new worksheet into your Excel file and name it "network". Go back to the previous sheet and select the entire matrix and copy it. Go to you new worksheet and click on the A1 cell in the upper left. Select "Paste special" from the "Home" tab. In the window that appears, check the box for "Transpose". This will paste your data with the columns transposed to rows and vice versa. This is necessary because we want the transcription factors that are the "regulatORS" across the top and the "regulatEES" along the side.
#* The labels for the genes in the columns and rows need to match. Thus, delete the "p" from each of the gene names in the columns. Adjust the case of the labels to make them all upper case.
#* In cell A1, copy and paste the text "rows genes affected/cols genes controlling".
#* Finally, for ease of working with the adjacency matrix in Excel, we want to alphabatize the gene labels both across the top and side.
#** Select the area of the entire adjacency matrix.
#** Click the Data tab and click the custom sort button.
#** Sort Column A alphabetically, being sure to exclude the header row.
#** Now sort row 1 from left to right, excluding cell A1. In the Custom Sort window, click on the options button and select sort left to right, excluding column 1.
#* Name the worksheet containing your organized adjacency matrix "network" and Save.
# Now we will visualize what these gene regulatory networks look like with the GRNsight software.
#* Go to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Select the menu item File > Open and select the regulation matrix .xlsx file that has the "network" worksheet in it that you formatted above. If the file has been formatted properly, GRNsight should automatically create a graph of your network. Move the nodes (genes) around until you get a layout that you like and take a screenshot of the results. Paste it into your PowerPoint presentation.

==== Summary of what you need to turn in for the individual Week 10 assignment ====

# Your individual journal page should have an '''''electronic lab notebook''''' recording your work. This includes the detailed methods specific to your analysis, your result files, the answers to any questions posed in the protocol above, a scientific conclusion, and the acknowledgments and references sections. Don't forget your paragraph which is a biological interpretation of your stem results.
# Upload your updated Excel spreadsheet to the wiki that has today's manipulations in it. Use the same filename as before so that the download link that you already (previous versions will still be available in the history).
# Append the screenshots of the stem results to the PowerPoint presentation that contains the p value table that you created for the [[Week 8]] assignments. Each slide in the presentation should have a meaningful title that describes the main message of the slide.
# Zip together all of the tab-delimited text files that you created for and from stem and upload them to the wiki.
#* the file that was saved from your original spreadsheet that you used to run stem
#* each of the genelist and GOlist files for each of your significant profiles.
# Write a paragraph-length conclusion for this week's exercise.

== Shared Journal Assignment ==

* Store your journal entry in the shared [[Class Journal Week 10]] 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).

=== Reflect ===

This week marks the end of Part 2 "Going Deeper" unit of the course. At this point in the semester, you have worked with 8 other people in the class as partners on journal assignments. Next week, you will be placed on teams of four that you will stay with throughout the rest of the semester. Ultimately the teams will be assigned by Drs. Dahlquist and Dionsio based on balancing areas of expertise amongst the team members. However, we will also be gathering your input into the formation of the teams. In class on Thursday, November 2, you will confidentially fill out a card giving us the names of three other people in the class whom you want to be on your team (you can also choose people that haven't been your journal partner yet) and one person whom you prefer not to be on your team.

As we get ready for the team projects, we are asking you to reflect upon working in teams either in this class or in previous classes.

# What kinds of characteristics do you want in your teammates, and why?
# What kinds of things make teamwork go smoothly?
# What kinds of things make teamwork not go so smoothly?

[[Category:Assignment]]

GRNsight Gene Page Project Deliverables

2017-11-21T00:26:24Z

Kdahlquist: /* PowerPoint Presentation */ details on PowerPoint.

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
# Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Code (GitHub pull request)
#* Each team should coordinate in performing a final integration and integration testing iteration (see [[Coder]] milestone for details) which the Interaction and Integration team then submits to the ''original'' GRNsight GitHub repository as a single, unified pull request from the class project’s fork
# Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of screenshots of stem results (''.pptx'')
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
# YEASTRACT "rank by TF" results (''.xlsx'')
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
# GRNmap output workbook (''.xlsx'')
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

== 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. 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 and should be 3-5 pages long (double-spaced). 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
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page 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 GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== 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.

Create a combined flow chart of the tasks/milestones of each of the team members (coders, QA, data analyst) and then describe the flow chart in the text. You should provide citations to the individual electronic notebooks of the team members as appropriate in the text so that the reader knows where to go for additional details.

=== 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.

==== Results of Microarray Data Analysis ====

* Table of ANOVA results from the [[Week 8]], discussing the interpretation of the p values.
* From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the ones you interpreted for the [[Week 10]] journal assignment.
** Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
** Discuss what the p values for the cluster and for the GO term list mean.
** Discuss the biological interpretation of your GO terms.
* Include a table that lists the transcription factors in your final network and their enrichment p value from YEASTRACT.
** Describe how and why you and your partner chose these transcription factors for your network.
** Include a figure (screenshot) of the unweighted networks visualized with GRNsight.
* Show the GRNsight visualization (screenshot) of the weighted networks, making sure that the genes are placed in the same relative location as each other an as the unweighted network figure.
* Interpret the results of the model as visualized in GRNsight.

==== Coding Results ====

* Give a narrative description of the new features created by the Coders.
** Provide code snippets and/or screenshots to illustrate as necessary.

=== Discussion ===

* Overall, what have you learned about the regulation of cold shock in yeast?
* How does the new feature facilitate the data analysis?
* Relate the results of your project to the papers you presented for journal club in [[Week 11]] (Coders) and [[Week 12]] (Data Analyst/QA).
** Did you discover anything new that wasn't reported in the journal club paper (Data Analyst/QA)?

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* 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_Fall2017_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 the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== 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 12 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:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be 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.

== 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 your team’s portion of the GRNsight Gene Page 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?

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]