Skinny Genes Deliverables

2019-12-07T21:46:37Z

Msamdars: Add more deliverables

{{Skinny Genes}}

==Data/Files==
# 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 Dr. Dahlquist)
# Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Sample-data relationship table in Excel (''.xlsx'')
#* [[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
# 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'')
#* [[Media: Ymesfin_Barreto_GRNmap_input.xlsx | GRNmap Input]]
# GRNmap output workbook (''.xlsx'') and output plots (''.jpg'') zipped together
#* [[Media: Ymesfin_Barreto_GRNmap_Output.zip | GRNmap Output]]
# MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
#* [[Media:BIOL 478 - BioDB CombinedDatabase.zip|MS Access database]]
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
#* [[Media:SkinnyGenesDatabaseREADME.pdf|Database README]]
# Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
# Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.

*[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Results]]

Skinny Genes Deliverables

2019-12-07T21:43:59Z

Msamdars: /* Data/Files */ add readme

{{Skinny Genes}}

==Data/Files==
# 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 Dr. Dahlquist)
# Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Sample-data relationship table in Excel (''.xlsx'')
#* [[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
# 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'') and output plots (''.jpg'') zipped together
# MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
#* [[Media:BIOL 478 - BioDB CombinedDatabase.zip|MS Access database]]
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
#* [[Media:SkinnyGenesDatabaseREADME.pdf|Database README]]
# Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
# Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.

*[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Results]]

File:SkinnyGenesDatabaseREADME.pdf

2019-12-07T21:42:58Z

Msamdars:

Skinny Genes Deliverables

2019-12-07T20:31:50Z

Msamdars: /* Data/Files */ add database

{{Skinny Genes}}

==Data/Files==
# 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 Dr. Dahlquist)
# Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Sample-data relationship table in Excel (''.xlsx'')
#* [[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
# 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'') and output plots (''.jpg'') zipped together
# MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
#* [[Media:BIOL 478 - BioDB CombinedDatabase.zip|MS Access database]]
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
# Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
# Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.

*[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Results]]

Skinny Genes Deliverables

2019-12-07T20:30:45Z

Msamdars: /* Data/Files */ add stuff

{{Skinny Genes}}

==Data/Files==
# 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 Dr. Dahlquist)
# Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Sample-data relationship table in Excel (''.xlsx'')
#* [[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample-Data Relationship Table]]
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
# 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'') and output plots (''.jpg'') zipped together
# MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
# Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
# Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.

*[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Results]]

File:BIOL 478 - BioDB CombinedDatabase.zip

2019-12-06T00:13:17Z

Msamdars: Msamdars uploaded a new version of File:BIOL 478 - BioDB CombinedDatabase.zip

Main Page

2019-12-04T00:01:56Z

Msamdars: /* Announcements */ add combined database

__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 367-01: Biological Databases'''</div>
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Fall 2019</div>

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

== Announcements ==

* Please complete the course evaluation on [http://brightspace.lmu.edu Brightspace] by class time on Thursday.
* Data Analysts and QA's who have a partner in their group can have a shared ''individual'' journal entry. Both students will be given the same grade and are expected to contribute equally to the electronic lab notebook.

* '''The combined database may be found [[Media:BIOL 478 - BioDB CombinedDatabase.zip|here]].'''

=== Upcoming Seminars ===

* '''LMU Society of Physics Students:''' Wednesday, December 4, 4:30 - 6:00 pm, Von der Ahe 190, Dr. Brian Keating, author of ''Losing the Nobel Prize'' will engage students with his research on imaging the cosmic background radiation, a remnant of the Big Bang.

== Instructor ==
* [[User:Kdahlquist|Kam D. Dahlquist]]

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:Marmas|Michael Armas]]
| style="padding-right: 1em" | [[User:Cdomin12|Christina Dominguez]]
| style="padding-right: 1em" | [[User:knguye66|Kaitlyn Nguyen]]
| style="padding-right: 1em" | [[User:Ntesfaio|Naomi Tesfaiohannes]]
|-
| style="padding-right: 1em" | [[User:mavila9|Marcus Avila]]
| style="padding-right: 1em" | [[User:Imacarae|Ivy-Quynh Macaraeg]]
| style="padding-right: 1em" | [[User:Jnimmers| John Nimmers-Minor]]
| style="padding-right: 1em" | [[User:eyoung20|Emma Young]]
|-
| style="padding-right: 1em" | [[User:Jcowan4|Jonar Cowan]]
| style="padding-right: 1em" | [[User:Dmadere | DeLisa Madere]]
| style="padding-right: 1em" | [[User:dramir36| David Ramirez]]
| style="padding-right: 1em" |
|-
| style="padding-right: 1em" | [[User:Icrespin| Iliana Crespin]]
| style="padding-right: 1em" | [[User:ymesfin| Yeabsira Mesfin]]
| style="padding-right: 1em" | [[User:msamdars| Mihir Samdarshi]]
| style="padding-right: 1em" |
|}

{{Final 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 Thursdays at 12:01am. In cases where subsequent revisions or corrections will be accepted, the instructor will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.

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

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/27/2019
|
|
* 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/>8/29/2019
| [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

** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/3/2019
|
|
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

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

[[Class Journal Week 2]]

|-
!
| Thursday<br/>9/5/2019
|
* [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']
* [http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]
* 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''

|
* DNA structure
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/10/2019
|
|
* Aipotu work session

| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]

|-
!
| Thursday<br/>9/12/2019
|
|
* Genes as models
* 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.
** [http://brightspace.lmu.edu Slides on Brightspace]
* [[Media:BIOL367_Fall2019_GeneticCode-CentralModel-2.pdf | Paper and pencil exercise]]

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/17/2019
|
* [http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford, Paul. “What is Code?” ''Business Week'', June 11, 2015.]
* [https://www.dataone.org/sites/all/documents/education-modules/pptx/L01_DataManagement.pptx DataONE: Data Management Slides]
|
Introduction to biological databases (part 1)
* What is bioinformatics?
* Open Science Ecosystem
* DataONE: Data Management and the life cycle of data
* Slides are on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]

|-
!
| Thursday<br/>9/19/2019
|
| Introduction to biological databases (part 2)
* [http://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
* Slides are on [http://brightspace.lmu.edu Brightspace]
* 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

{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/24/2019
|
|
[[ Week 4]] work session
| rowspan="2" | [[Week 5]]
(individual due at 12:01am 10/1)

'''''Note Tuesday Due Date'''''

[[Class Journal Week 5]]

(shared due at 12:01am 10/3)

|-
!
| Thursday<br/>9/26/2019
| [https://academic.oup.com/nar/article/47/D1/D1/5280358 The 26th 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)
* Terminology, types, evaluation, four "Gold Standard" databases
* 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]
* [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace]

{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/1/2019
|
| Database presentations part 1
# group 1
# group 2
# group 3
# group 4
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/3/2019
|
| Database presentations part 2
# group 1
# group 2
# group 3

[[Presentation Rubric]]

[http://brightspace.lmu.edu/ Presentation Guidelines on Brightspace]

|}

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

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/8/2019
| 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'']
|
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]

|-
!
| Thursday<br/>10/10/2019
| [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.]
| Review [[Week 6]] assignment

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/15/2019
| [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]
| More about DNA microarray analysis
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/17/2019
|
| Begin DNA microarray analysis 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/>10/22/2019
| [https://academic.oup.com/bioinformatics/article/21/suppl_1/i159/203147 Ernst & Bar-Joseph (2006) STEM: a tool for the analysis of short time series gene expression data.]
|
Microarray Data Analysis part 2
* Clustering with stem software



| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]

|-
!
| Thursday<br/>10/24/2019
|
* [https://academic.oup.com/nar/article/46/D1/D348/4191333 Teixeira, et al. (2017). YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in ''Saccharomyces cerevisiae'']
* [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 3
* Finding a candidate GRN ([http://www.yeastract.com/ YEASTRACT])

{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/29/2019
| [https://link.springer.com/article/10.1007/s11538-015-0092-6 Dahlquist et al. (2015) Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in ''Saccharomyces cerevisiae'']
|
Microarray Data Analysis part 4
* Visualizing the candidate GRN ([https://dondi.github.io/GRNsight/ GRNsight])
* Dynamical systems modeling of the gene regulatory network ([http://kdahlquist.github.io/GRNmap/ GRNmap])

| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>10/31/2019
|
|
Microarray Data Analysis part 5
* Visualizing and interpreting the modeling results ([https://dondi.github.io/GRNsight/ GRNsight])
* Group requests due in class (collected on notecards)
|}

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

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/5/2019
|
| Dynamical Systems Modeling with GRNmap
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)

'''''Thursday Due Date'''''
|-
!
| Thursday<br/>11/7/2019
|
|
Begin GRNsight Expression Database Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/12/2019
|
|
Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

| rowspan="2" | [[Week 12/13]]

(due at 12:01am 11/26)

'''''Note Tuesday Due Date'''''

|-
!
| Thursday<br/>11/14/2019
|
| Journal Club Presentations

[[Presentation Rubric]]

[http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace]

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/19/2019
|
|
* Status report
* Work session

| rowspan="2" | [[Week 12/13]]

(due at 12:01am 11/26)<br/>
'''''Note Tuesday due date'''''
|-
!
| Thursday<br/>11/21/2019
|
|
* Status report
* Work session

|-
! 14
| Tuesday<br/>11/26/2017
|
|
* Status report
* Work session
| '''''No Week 14 assignment'''''
|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/28/2019
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/3/2019
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:00pm 12/13)
|-
!
| Thursday<br/>12/5/2019
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/10/2019
| 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/>12/13/2019 4:00 PM
|
| '''Project deliverables due 4:00 PM'''
|
|}

== Course Information ==

=== Instructor ===

==== [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]] ====
: http://kdahlquist.github.io/DahlquistLab/index.htm
: '''Phone:''' (310) 338-7697
: '''E-mail:''' kdahlquist at lmu dot edu
: '''Office:''' Life Sciences Building 289
: '''Office Hours (Fall 2019):''' Mondays & Wednesdays 2:00-3:00 PM, Tuesdays & Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

=== 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 instructor should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

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

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructor 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 instructor 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 [https://studentaffairs.lmu.edu/media/studentaffairs/osccr/documents/1920-LMU-community-standards.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/fall2019/. 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 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 instructor at night or on the weekend will be answered the next school day.

=== 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 ===

Your work in this course will be assessed in the following 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" | 50
| 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" | '''420'''
| '''points'''
|}

Final course grading scale:
94.0-100.0% A
90.0- 93.9% A-
86.0- 89.9% B+
82.0- 85.9% B
78.0- 81.9% B-
74.0- 77.9% C+
70.0- 73.9% C
67.0- 69.9% C-
60.0- 66.9% D
≤ 59.9% F

Current grades will be made available at [http://brightspace.lmu.edu Brightspace].

==== 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 transferable to other applications.

You will create an individual user page and make weekly entries that the instructor 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 Thursday 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 instructor 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". You will be expected to consult with your partner 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. Specific instructions will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:00pm. 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 Biology Department seminars 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 Department seminars may be approved in advance for extra credit at the instructor's 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. '''''The minimum penalty for an instance of academic dishonesty in this course, even on a 1-point assignment or extra credit assignment, is a one-letter grade penalty in the course and a zero on the assignment.''''' 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.

You are required to sign the [[Media:BIOL367_Fall2019_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]] for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2019_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_Fall2019_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html 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 instructor early in the semester to discuss any accommodations for this course for which you have been approved.

=== Health and Wellness ===

There are many resources for student wellness on campus. A central website for students is: http://lionwellness.lmu.edu.

=== Emergency Preparedness ===

To report an emergency or suspicious activity, contact the LMU Department of Public Safety by phone (x222 or 310-338-2894) or at the nearest emergency call box. In the event of an evacuation, follow the evacuation signage throughout the building to the designated safe refuge area where you will receive further instruction from Public Safety or a Building Captain. For more safety information and preparedness tips, visit http://www.lmu.edu/emergency.

=== 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/fall2019/.

File:BIOL 478 - BioDB CombinedDatabase.zip

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Skinny Genes Deliverables

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Skinny Genes Deliverables

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{Skinny Genes}

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{| class="wikitable" style="width: 100%; text-align: center"
! colspan="10"|Skinny Genes Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[Skinny Genes|Skinny Genes Project]]
! rowspan="2"|[[Template:Skinny Genes|Skinny Genes Template Page]]
! rowspan="2"|[[Skinny Genes Deliverables|Skinny Genes Deliverables]]
! Members
| '''Project Manager & Data Analysis: '''[[User:ymesfin| Yeabsira Mesfin]]
| [[Skinny Genes Quality Assurance|'''Quality Assurance''']]''':''' [[User:Jcowan4|Jonar Cowan]] & [[User:Cdomin12|Christina Dominguez]]
| '''Data Analysis:''' [[User:dramir36| David Ramirez]]
| '''Coder:''' [[User:msamdars| Mihir Samdarshi]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

[[Category:Skinny Genes]]

[[Category:Group Projects]]

Template:Skinny Genes

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Msamdars: add Deliverables

{| class="wikitable" style="width: 100%; text-align: center"
! colspan="8"|Skinny Genes Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[Skinny Genes|Skinny Genes Project]]
! rowspan="2"|[[Template:Skinny Genes|Skinny Genes Template Page]]
! rowspan="2"|[[Skinny Genes Deliverables|Skinny Genes Deliverables]]
! Members
| '''Project Manager & Data Analysis: '''[[User:ymesfin| Yeabsira Mesfin]]
| [[Skinny Genes Quality Assurance|'''Quality Assurance''']]''':''' [[User:Jcowan4|Jonar Cowan]] & [[User:Cdomin12|Christina Dominguez]]
| '''Data Analysis:''' [[User:dramir36| David Ramirez]]
| '''Coder:''' [[User:msamdars| Mihir Samdarshi]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

[[Category:Skinny Genes]]

[[Category:Group Projects]]

Skinny Genes

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Msamdars: /* Files */ add db

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Sample_to_Data_Relationship_Table.xlsx | Sample to Data Relationship Table]]

[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

[[Media: Ymesfin_Barreto_ANOVA_no_duplicates_-_Copy.xlsx | ANOVA Data (no duplicates)]]

[[Media:Ymesfin Barreto ANOVA no duplicates and revised headers.xlsx | ANOVA Data (most updated no duplicates, new headers)]]

[[Media: Copy_ymesfin_Baretto_yeastract_regulation_matrix.xlsx | Network Data]]

[[Media: Ymesfin_Results.pdf ‎| Stem and GRNsight Network]]

[[Media: Skinny Genes Database.zip|Zip file containing the Skinny Genes group database]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in Saccharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548
#David: Gladfelter, A.S., Kozubowski, L., Zyla, T.R., and Lew, D.J. (2005) Interplay between septin organization, cell cycle and cell shape in yeast. J Cell Sci 118: 1617–1628. DOI: 10.1242/jcs.02286
#David: Howell, A.S., and Lew, D.J. (2012) Morphogenesis and the cell cycle. Genetics 190: 51–77. DOI: 10.1534/genetics.111.128314
#Jonar: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS biology, 4(11), e351.
#Jonar: Udensi, U. K., & Tchounwou, P. B. (2017). Potassium Homeostasis, Oxidative Stress, and Human Disease. International journal of clinical and experimental physiology, 4(3), 111–122. doi:10.4103/ijcep.ijcep_43_17

==Schedule==
{| class="wikitable"
|-
! Tasks
! Date
|-
| Team Journal Assignment: Methods and Results thus far
*Project Manager: Create Sample/Data Relationship Table
*Data Analysis: download raw data, run ANOVA
*QA and Coder: standardize the ID and Standard Names of the genes
| 11/21/19
|-
|
| 11/26/19
|-
|
| 11/28/19
|-
|
| 12/03/19
|-
|
| 12/05/19
|-
| Final Presentation
| 12/10/19
|-
| Report submitted
| 12/13/19
|-
|}

==Executive Summaries==
===Week 11===
====Aby's Reflection====
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.
====Jonar's Reflection====
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)
====Christina's Reflection====
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

[[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 00:51, 26 November 2019 (PST)

====Mihir's Reflection====
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)
====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:01, 26 November 2019 (PST)

===Week 12/13===
====Aby's Reflection====
*Progress: This week David and I statistically analyzed the data using an ANOVA.
*#What worked? The ANOVA was relatively easy to code using Excel.
*#What didn't work? We were hoping to run STEM this week as well but had difficulty creating the ID's and Standard Names for the data.
*#What will I do next to fix what didn't work? We reached out to Dr. Dahlquist in regards to changing the ID's and Standard Names and thus, we should be able to run STEM after a few more edits.
[[User:Ymesfin|Ymesfin]] ([[User talk:Ymesfin|talk]]) 11:10, 25 November 2019 (PST)

====Jonar's Reflection====
*Progress:
*#What worked? What worked was how we divided what needed to be done and how we were in constant communication with each other.
*#What didn't work? Early on we had problems with the standard name and gene ID, which caused us to get a little anxious about what were supposed to do. In essence, we needed to ask for help. (Which was done later on but not early enough)
*#What will I do next to fix what didn't work? Overall, I think we are handling the project well but if we had to work on something it would probably better timing for project management.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 19:25, 25 November 2019 (PST)

====Christina's Reflection====
*Progress:
*#What worked? We were able to communicate in class to effectively figure out what we needs to be done on a timeline.
*#What didn't work? It took a long to get past the step of finalizing the data into columns that had both the IDs and standard names. However, this was due to the fact that the data sheet had many repeated genes and a variety of different names for genes.
*#What will I do next to fix what didn't work? Communicate better on how we can solve this problem as a group.

====Mihir's Reflection====
*Progress:
** This week I worked on creating the format for encoding the entries into the database.

#What worked?
#*This weekend we split up into our different guilds. I think that we worked well in those guilds, and it seemed like the pairs of Jonar and Christina and David and Aby worked well.
#What didn't work?
#*I think that this week, we were a little too fractured because of how immediately we were required to split up following the official beginning of the project. There was a lack of communication when we were discussing how to fix the gene names of the spreadsheet. Even though our communication was good last week, because of a variety of reasons I think that we were not able to effectively relate information regarding our data and formatting to one another.
#What will I do next to fix what didn't work?
#*I think this next week, we should take the time talk to each other regarding what he had accomplished between work sessions and what we planned on working on during the upcoming work session.

====David's Reflection====
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:02, 26 November 2019 (PST)

==Milestones==

====Milestones 1====
====Milestones 2====
====Milestones 3====
====Milestones 4====
====Milestones 5====
====Milestones 6====
====Milestones 7====

File:Skinny Genes Database.zip

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Template:Skinny Genes

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Msamdars: update /clean template

{| class="wikitable" style="width: 100%; text-align: center"
! colspan="8"|Skinny Genes Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[Skinny Genes|Skinny Genes Project]]
! rowspan="2"|[[Template:Skinny Genes|Skinny Genes Template Page]]
! Members
| '''Project Manager & Data Analysis: '''[[User:ymesfin| Yeabsira Mesfin]]
| [[Skinny Genes Quality Assurance|'''Quality Assurance''']]''':''' [[User:Jcowan4|Jonar Cowan]] & [[User:Cdomin12|Christina Dominguez]]
| '''Data Analysis:''' [[User:dramir36| David Ramirez]]
| '''Coder:''' [[User:msamdars| Mihir Samdarshi]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

[[Category:Skinny Genes]]

[[Category:Group Projects]]

Category:Skinny Genes

2019-11-26T07:59:17Z

Msamdars: Created page with "Skinny Genes (levi's)"

Skinny Genes

(levi's)

Msamdars Week 12/13

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Msamdars: /* Purpose */ update notebook

==Electronic Lab Notebook==
===Purpose===
This is the electronic notebook recording information regarding my progress towards the final project. I am a member of the designer/coder guild and will be designing the database. Furthermore, I will be helping my group to add and analyze our data from the Barreto et al. paper "The short‐term response of yeast to potassium starvation" (2012).

===Methods===
*Decided with the help of the group will be using the Azure platform to host a centralized server on which we can all access the Microsoft Access Database.
*Furthermore, we decided on the format for the metadata sheet and the individual data sheets for each article.
**Sample To Data Table:
**#Sample ID (PMID + index)[integer]
**#Pubmed ID [integer]
**#Control Yeast Strain [string]
**#Control [String]
**#Concentration Value [Integer]
**#Concentration Unit [String]
**#Time Value [Integer]
**#Time Units [String]
**#Number of Replicates [Integer]
**Citation Table:
**#PMID [Integer]
**#Authors [Array[strings]]
**#Title [String]
**#DOI [String]
**#NCBI GEO ID [Integer]
*Attempted to write program using downloaded gene list from Saccharomyces Gene Database. Wrote program using Pandas and NumPy libraries in a Python Jupyter Notebook. Gave up on realizing it was doomed.
*Used the [http://llama.mshri.on.ca/synergizer/translate/ Synergizer] website, which was not helpful at all and was not giving the right ids or names.
*Emailed Dr. Dahlquist for help. Received edited gene list.

===Conclusion===
This week we designed the main part of the database. Next week, I will work on standardizing the expression sheet tables. Furthermore, I will start to build it out in Microsoft Access.

==Data & Files==
[[File:Metadata Sheet.xlsx|The metadata sheet with all appropriate sheets]]

==Acknowledgments==
This week my team members are in [[Skinny_Genes|Skinny Genes]] which is composed of [[User:Jcowan4|Jonar Cowan]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]], & [[User:Msamdars|myself]]. We worked in and out of class together.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source

==Other Links==
{{Template:msamdars}}

==References==
# LMU BioDB 2019. (2019). Week 12. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
# MediaWiki (2019). Category: Help. Retrieved November 25, 2019, from https://www.mediawiki.org/wiki/Category:Help

[[Category:Group Projects]]
[[Category:Skinny Genes]]

Msamdars Week 12/13

2019-11-26T07:56:53Z

Msamdars: /* Electronic Lab Notebook */ add entries

==Electronic Lab Notebook==
===Purpose===
This is the electronic notebook recording information regarding my progress towards the final project. I am a member of the designer/coder guild and will be designing the database.

===Methods===
*Decided with the help of the group will be using the Azure platform to host a centralized server on which we can all access the Microsoft Access Database.
*Furthermore, we decided on the format for the metadata sheet and the individual data sheets for each article.
**Sample To Data Table:
**#Sample ID (PMID + index)[integer]
**#Pubmed ID [integer]
**#Control Yeast Strain [string]
**#Control [String]
**#Concentration Value [Integer]
**#Concentration Unit [String]
**#Time Value [Integer]
**#Time Units [String]
**#Number of Replicates [Integer]
**Citation Table:
**#PMID [Integer]
**#Authors [Array[strings]]
**#Title [String]
**#DOI [String]
**#NCBI GEO ID [Integer]
*Attempted to write program using downloaded gene list from Saccharomyces Gene Database. Wrote program using Pandas and NumPy libraries in a Python Jupyter Notebook. Gave up on realizing it was doomed.
*Used the [http://llama.mshri.on.ca/synergizer/translate/ Synergizer] website, which was not helpful at all and was not giving the right ids or names.
*Emailed Dr. Dahlquist for help. Received edited gene list.

===Conclusion===
This week we designed the main part of the database. Next week, I will work on standardizing the expression sheet tables. Furthermore, I will start to build it out in Microsoft Access.

==Data & Files==
[[File:Metadata Sheet.xlsx|The metadata sheet with all appropriate sheets]]

==Acknowledgments==
This week my team members are in [[Skinny_Genes|Skinny Genes]] which is composed of [[User:Jcowan4|Jonar Cowan]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]], & [[User:Msamdars|myself]]. We worked in and out of class together.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source

==Other Links==
{{Template:msamdars}}

==References==
# LMU BioDB 2019. (2019). Week 12. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
# MediaWiki (2019). Category: Help. Retrieved November 25, 2019, from https://www.mediawiki.org/wiki/Category:Help

[[Category:Group Projects]]
[[Category:Skinny Genes]]

2019-11-19T02:13:55Z

Msamdars: /* Annotated Bibliography */ add bib

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', ''4''(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', ''15''(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', ''12''(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in S accharomyces cerevisiae. ''Molecular microbiology'', ''95''(3), 555-572. DOI: 10.1111/mmi.12886
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., … Kschischo, M. (2012). Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling. ''PLoS Computational Biology'', ''8''(6). doi: 10.1371/journal.pcbi.1002548

==Executive Summaries==
===Aby's Reflection===
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.

===Jonar's Reflection===
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)

===Christina's Reflection===
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

===Mihir's Reflection===
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)

===David's Reflection===
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 23:37, 13 November 2019 (PST)

Skinny Genes

2019-11-19T02:09:03Z

Msamdars: /* Annotated Bibliography */ add Mihir's

{{template:Skinny Genes}}
==Positions==

'''Project Manager:''' Aby

'''Quality Assurance:''' Jonar & Christina

'''Data Analysis:''' Aby & David

'''Coder:''' Mihir
==Files==
[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club_2.pdf | Journal Club Presentation]]

==Annotated Bibliography==
#Aby: Hess, D. C., Lu, W., Rabinowitz, J. D., & Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. ''PLoS biology'', 4(11), e351. DOI: 10.1371/journal.pbio.0040351
#Aby: Navarrete, C., Petrezsélyová, S., Barreto, L., Martínez, J. L., Zahrádka, J., Ariño, J., ... & Ramos, J. (2010). Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions. ''FEMS yeast research'', 10(5), 508-517. DOI: DOI:10.1111/j.1567-1364.2010.00630.x
#Christina: Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. ''BMC genomics'', 15(1), 1040. doi:10.1186/1471-2164-15-1040
#Christina: Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. ''FEMS yeast research'', 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
#Mihir: Canadell, D., González, A., Casado, C., & Ariño, J. (2015). Functional interactions between potassium and phosphate homeostasis in S accharomyces cerevisiae. ''Molecular microbiology'', 95(3), 555-572.
#Mihir: Kahm, M., Navarrete, C., Llopis-Torregrosa, V., Herrera, R., Barreto, L., Yenush, L., ... & Kschischo, M. (2012). Potassium starvation in yeast: mechanisms of homeostasis revealed by mathematical modeling. ''PLoS computational biology'', 8(6), e1002548.

==Executive Summaries==
===Aby's Reflection===
*Progress: This week we created an outline for our presentation and formatted the presentation for the journal club.
*#What worked? Responsibilities for the presentation was delegated well so that everyone contributed an equal share.
*#What didn't work? It was difficult to work around everyone's schedules so that we could meet up and work together.
*#What will I do next to fix what didn't work? We will need to communicate with one another better and anticipate the amount of time necessary to complete the assignment as a group so that our schedules don't interfere with the groupwork.

===Jonar's Reflection===
*Progress:
*#What worked? Everybody in the group was responsive and we were able to agree on and start our presentation early. The delegation of work and support worked well.
*#What didn't work? Due to time constraints with multiple people, finding time for all five members was a little difficult
*#What will I do next to fix what didn't work? We can plan an early meeting time or we can delegate tasks and plan a little meeting just to go over the work.

[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 23:59, 13 November 2019 (PST)

===Christina's Reflection===
*Progress:
*#What worked? We started early which allowed us to have the time to work through our presentation in a timely manner.
*#What didn't work? It is difficult to find a meeting time for 5 people in order to work on the presentation.
*#What will I do next to fix what didn't work? Try to find a time on the weekend to meet instead of on school days.

===Mihir's Reflection===
*Progress:
*#What worked?
*#* We were able to communicate well, and we all worked together to help each other understand and excel in our tasks. Furthermore, we figured out methods of communication and how to best work with each other remotely.
*#What didn't work?
*#* Scheduling times to work on this assignment was pretty hectic this week, given that each member of our team had an unusual number of projects, midterms, homework, and extra-curricular activities this week. We could not all meet together outside of class.
*#What will I do next to fix what didn't work?
*#* Hopefully, this was a one-time occurrence and none of us will be as busy as we were this week. However, other than that, we could also improve our responsiveness in our team's group message, as that is our sole method of communication outside of class.
[[User:Msamdars|Msamdars]] ([[User talk:Msamdars|talk]]) 20:16, 13 November 2019 (PST)

===David's Reflection===
*Progress:
*#'''What worked?''' We were able to communicate and agree to meet twice outside of class, which was the most we could do during our busy schedules. We were also able to create a GroupMe group chat so that everyone has a chance to communicate with each other and ask questions when needed.
*#'''What didn't work?''' Creating times where we could all meet up in the computer lab was very difficult because all of us had different schedules, so when we actually did make a time to meet, we made sure to use the time together as effective as possible. I wish I didn't have so much work from other classes that coincidentally built up especially in this week.
*#'''What will I do next to fix what didn't work?''' I will try to better manage my time and spending time on assignments from other classes evenly so that when it comes to working on this project with the group, I can fully focus on what I have to do instead of stressing about another project from another class.
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 23:37, 13 November 2019 (PST)

Msamdars Week 11

2019-11-19T00:24:51Z

Msamdars: /* Annotated Bibliography */ add template

==Purpose==
This week in our assignment we will read and analyze a scientific article and be able to explain the results to others. Furthermore, we will also be working in our teams for the first time and learn to navigate the team's dynamics.

==Ten Definitions==

retrograde pathway - Signals that travel from plastids to nuclei in plants and eukaryotic algae, and from mitochondria to nuclei in other eukaryotes, and tend to send messages regarding stress and environmental sensing (Lagarias et al., 2013)

septin ring - Septins are GTP-binding proteins in most eukaryotic cells (except in plant cells) and can form a protein complex in the shape of nonpolar filaments, filament bundles, rings, or cages (Douglas et al., 2005)

trehalose - A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates (Biology Online, 2019)

immunoblot - (AKA Western Blot) A procedure in which proteins separated by electrophoresis in polyacrylamide gels are transferred (blotted) onto nitrocellulose or nylon membranes and identified by specific complexing with antibodies that are either pre-or post-tagged with a labelled secondary protein. (Biology Online, 2019)

triose phosphate - (AKA Glyceraldehyde phosphate) A phosphate ester of the 3-carbon sugar glyceraldehyde and has chemical formula: C3H7O6P (Biology Online, 2019)

chemostat - Apparatus for maintaining a bacterial population in the exponential phase of growth by regulating the input of a rate-limiting nutrient and the removal of medium and cells (Smith, 2000)

Cdc11 - One of a family of mitotic septins that aid in cell division by forming a ring structure at the septum (Biology Online, 2019)

RT-PCR - Reverse transcriptase polymerase chain reaction; reverse transcription PCR PCR in which the starting template is RNA, implying the need for an initial reverse transcriptase step to make a DNA template. Some thermostable polymerases have appreciable reverse transcriptase activity; however, it is more common to perform an explicit reverse transcription, inactivate the reverse transcriptase or purify the product, and proceed to a separate conventional PCR. Abbreviation ambiguous because also used sloppily for real-time PCR. (Lackie, 2007)

bud neck - The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.

isozyme - (AKA Isoenzyme) Enzymes that differ in amino acid sequence but catalyze the same chemical reaction. These enzymes usually display different kinetic parameters (i.e. different KM values), or different regulatory properties. The existence of isozymes permits the fine-tuning of metabolism to meet the particular needs of a given tissue or developmental stage (Biology Online, 2019)

==Journal Article Outline==
===What is the main result presented in this paper?===
The main result of the paper states that short-term potassium deprivation has an effect on the mRNA transcription rate of around a thousand genes. They see that in particular genes that control sulfur metabolism, trigger an oxidative response, and activate the retrograde pathway get affected. It also says that they observe a significant decrease in overall ribosome creation and translation, components like cyclins and protein kinases, and decrease in septin assembly.

===What is the importance or significance of this work?===
Given that a lack of potassium showed a significant decrease in gene expression of certain pathways, this opens up a new field of study to see how exactly the potassium cation regulates these pathways.

===What were the limitations in previous studies that led them to perform this work?===
This study had apparently never been done before. Thus, this study was necessitated to perform a complete transcriptomic analysis.

===How did they treat the yeast cells (what experiment were they doing?)===
The scientists grew the cells at 28C in translucent K+ free medium supplemented with KCl solution. Cells were then transferred to fresh media with KCl, or without K+. Samples of both were then taken at 20, 40, 60, and 120 min from four replicates.

===What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?===
The strains used were BY4741, BYT1, BYT2, BYT12, BY4741 rtg2, BY4741 rtg3, BY4741 fzo1, YNR055.1 YPC722 (5), YPC723, YPC724, W303-1A, DBY746. It was not told to us which ploidy each strain was. However, according to the SGD wiki, BY4741 is a haploid strain (Cherry et al., 2011).

===What media did they grow them in? What temperature? What type of incubator? For how long?===
The yeast were grown in translucent potassium-free YNB media at 28°C supplemented with 50 mM KCl. They did not specify an incubator, but did say the yeast was grown until the culture reached an optical density of 0.8.

===What controls did they use?===
They extracted a control from four replicates from the media supplemented with 50 mM KCl at every timepoints of the experiment.

===How many replicates did they perform per treatment or timepoint?===
They used four replicates of each experimental treatment and control at each timepoints of 0, 20, 40, 60, 120.

===What method did they use to prepare the RNA, label it and hybridize it to the microarray?===
They used the Ribo-Pure kit to extract the RNA, and didn't say how they labelled and hybridized it.

===What mathematical/statistical method did they use to analyze the data?===
They used GEPAS server to pre-process the microarray data, but made no mention of what mathematical approaches they used. For metabolite data, they used the DataAnalysis software and used standardized calibration curves to quantify the metabolites.

===Are the data publicly available for download? From which web site?===
Yes, the data is available at the Society of Applied Microbiology website.

===Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.===
# Figure 1
#* This figure shows the results of clustering of the genes. One can see overall trends of genes tend to be of either repression or activation across all of the timepoints. One can see that there are no other trends, with clusters of genes increasing expression at one timepoints and decreasing expression at another timepoint.
# Table 1
#* This table simply shows the number of genes activated and repressed at each of the timepoints of the experiments.
# Figure 2
#* There are multiple parts to this figure.
#** A) is a figure of sulfur uptake, and Met/Cys metabolism, with the genes associated annotated.
#** B) shows graphs of mRNA level of a number of genes over time for both treatments. X-Axis: mRNA change (log-fold expression); Y-Axis: genes (by name). Measurements from microarray data.
#** C) shows graphs of intracellular levels of Met and Cys over time after transfer of cells to K+-free medium. X-Axis: Time (min); Y-Axis: Met/Cys concentration μM. Measurements from HPLC-mass spectrometry.
# Figure 3
#* There are multiple parts to this figure.
#** A) shows a graph of the response of certain environmental-stress response genes over time. X-Axis: Time (min); Y-Axis: mRNA change (log-fold expression). Measurements from microarray data.
#** B) are images of stained cells that show the amount of ROS produced in each cell over the time of the experiment. This is shown by fluorescent dyes that activate upon exposure to ROS.
#** C) shows a graph of the concentration of oxidized and reduced forms of glutathione over over the course of the potassium-deprivation experiment in the cells. X-Axis: Time (min); Y-Axis: Glutathione concentration μM. Measurements from HPLC-mass spectrometry.
# Figure 4
#* There are multiple parts to this figure.
#** A) shows a diagram of methylglyoxal generation/degradation and trehalose metabolism pathways.
#** B) shows graphs of the changes in expression levels of genes associated with methylglyoxal generation/degradation and trehalose metabolism. X-Axis: Time (min); Y-Axis: mRNA change (log-fold expression). Measurements from microarray data.
#** C) shows levels of methylglyoxal within the cell over the course of the potassium-deprivation experiment. X-Axis: Time (min); Y-Axis: Methylglyoxal concentration μM. Measurements from HPLC-mass spectrometry.
# Figure 5
#* There are multiple parts to this figure.
#** A) shows the expression levels of certain genes controlling the retrograde response over time, accompanied by a picture of the results of RT-PCR on 3 genes, with a wild type and mutant. X-Axis: Time (min); Y-Axis: mRNA change (log-fold expression). Measurements from microarray data.
#** B) shows fluorescent microscopy images of mitochondrial morphology in wild type cells treated and untreated with KCl, and images of a mutant strain that act as a control.
#** C) shows concentrations of ammonium in wild type cells in K+-free medium and normal medium. X-Axis: Time (min); Y-Axis: NH4+ concentration nmol/mg. Measurement source unknown.
#** D) shows concentrations of ammonium in multiple mutant cells with different or knocked-down potassium transporters. X-Axis: Time (min); Y-Axis: NH4+ concentration nmol/mg. Measurement source unknown.
# Figure 6
#* There are multiple parts to this figure.
#** A) shows changes in expression of genes that control cyclins. X-Axis: Time (min); Y-Axis: mRNA change (log-fold expression). Measurements from microarray data.
#** B) shows images of cyclin mRNA quantified by RT-PCR, with two treatments at two timepoints each.
#** C) shows images of a western blot of multiple cyclins at a variety of timepoints.
# Figure 7
#* There are multiple parts to this figure.
#** A) shows changes in expression of genes related to bud neck and septin ring formation. X-Axis: Time (min); Y-Axis: mRNA change (log-fold expression). Measurements from microarray data.
#** B) shows fluorescent microscopy images of Cdc11-GFP in wild-type cells with and without K+ treatment.
#** C) shows images of a Western blot for Cdc11 at multiple timepoints in K+ free treatment and control, as well as in multiple forms, supernatant and pellet.
#** D) shows fluorescent microscopy images of wild type cells with Cdc11-GFP in them, treated with and without K+.
# Table 2
#* This table contains a list of all of the strains used in the study, the genotype of each strain, and the source/reference for each strain.

===How does this work compare with previous studies?===
There have been no previous studies that are equivalent to this study. No genome-wide transcriptomic analysis has been carried out like this, with this kind of stressor. Thus, this research is novel and illuminates the effects of a lack of potassium on cells.

===What are the important implications of this work?===
This study leaves a number of future studies available for study. We may see future studies into how potassium affects cell cycle regulation because it showed that cyclins are regulated by potassium. Furthermore, the retrograde response pathway and ammonium can also be targets of further study.

===What future directions should the authors take?===
I think that the authors should study the oxidative stress response and global environmental stress response, as these two were heavily touched on in the study. One may see that the authors studied the accumulation of methylglyoxal and how it affects the environmental stress response, and I would study that overall pathway.

===Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?===
I think that this paper was very thorough with how they presented all their results. Every significant result that the authors presented, they supported with additional follow-up experiments. I think that they presented quite a bit of information, and provided a solid baseline study for a number of future studies. I do not think there were any major flaws.

==Annotated Bibliography==
===Reference 1===
# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
# The link to the abstract from PubMed.
# The link to the full text of the article in PubMedCentral (if not available, write N/A).
# The link to the full text of the article (HTML format) from the publisher web site.
# The link to the full PDF version of the article from the publisher web site.
# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
# How is the article available to you?
#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
# Who is the publisher of the journal?
#* Is the publisher for-profit or non-profit?
#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
#* What country is the journal published in?
# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
# Are the articles in this journal peer-reviewed?
# Provide a link to the scientific advisory board/editorial board of the journal.
# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
# Is the article a review or primary research article?
# Are the data associated with this article available? If so, provide a link to the dataset.

===Reference 2===
# The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]), ''with DOI''.
# The link to the abstract from PubMed.
# The link to the full text of the article in PubMedCentral (if not available, write N/A).
# The link to the full text of the article (HTML format) from the publisher web site.
# The link to the full PDF version of the article from the publisher web site.
# Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
# How is the article available to you?
#* Is the article available “Open Access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If '''YES''', stop here.
#* If the article is not Open Access, is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If '''YES''', stop here.
#* Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: [http://sq4ya5rf2q.search.serialssolutions.com/ http://sq4ya5rf2q.search.serialssolutions.com/] If '''YES''', stop here.
#* Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: [https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99 https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99]. ''Note that you don’t need to actually request it for this assignment''.
# Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
# Who is the publisher of the journal?
#* Is the publisher for-profit or non-profit?
#* Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
#* Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
#* What country is the journal published in?
# How Long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
# Are the articles in this journal peer-reviewed?
# Provide a link to the scientific advisory board/editorial board of the journal.
# What is the journal impact factor? (Look to see if it is provided on the journal home page.)
# Is the article a review or primary research article?
# Are the data associated with this article available? If so, provide a link to the dataset.

===Responses
# PubMed
#* What original keyword(s) did you use? How many results did you get?
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
# Google Scholar
#* What original keyword(s) did you use? How many results did you get?
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
# Web of Science
#* What original keyword(s) did you use? How many results did you get?
#* Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
# Use the advanced search functions for each of these three databases/tools and answer the following:
# PubMed
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
# Google Scholar
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
# Web of Science
#* Which advanced search functions were most useful to narrow down the search? How many results did you get?
# Perform a prospective search on your article in the Web of Science and answer the following:
#* How many articles does this article cite?
#* How many articles cite this article?
* Reflect:
*# What impact does the choice of keywords have on your results?
*# What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?

==Data & Files==
[[Media: Ymesfin_Yeast_Potassium_Starvation_Journal_Club.pdf | Journal Club Presentation]]

==Conclusion==
This week we read a paper, and critically analyzed the paper. Furthermore, we learned to use resources to better supplement our knowledge, and to increase our information literacy. We learned to analyze those resources and think critically about them as well. I learned quite a bit during this assignment, and was surprised to learn that the first genome-wide transcriptomic analysis on yeast deprived of such an important cation was only carried out a few years ago. I wonder what other analogous experiments have not been carried out, as a result of this?

==Acknowledgments==
This week my team members are in [[Skinny_Genes|Skinny Genes]] which is composed of [[User:Jcowan4|Jonar Cowan]], [[User:Ymesfin|Aby Mesfin]], [[User:Dramir36 |David Ramirez]], [[User:Cdomin12|Christina Dominguez]], & [[User:Msamdars|myself]]. We worked in and out of class together.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

==Other Links==
{{msamdars}}
==References==
# LMU BioDB 2019. (2019). Week 11. Retrieved November 7, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
# MediaWiki (2019). Category: Help. Retrieved November 11, 2019, from https://www.mediawiki.org/wiki/Category:Help
# Lagarias, J.C., Duanmu, D., Casero, D., Dent, R.M., Gallaher, S., Yang, W., Rockwell, N.C., Martin, S.S., Pellegrini, M., Niyogi, K.K., Merchant, S.S., Grossman, A.R. (2013). "Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival". Proceedings of the National Academy of Sciences of the United States of America. 110 (9): 3621–3626. doi:10.1073/pnas.1222375110.
# Douglas, L. M., Alvarez, F. J., McCreary, C., & Konopka, J. B. (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12.
# Biology Online. (2019). Retrieved November 7, 2019 from https://biology-online.org
# Smith, A. (2000). Oxford Dictionary of Biochemistry and Molecular Biology: Revised Edition. Oxford University Press.
# Lackie, J. M. (Ed.). (2007). The dictionary of cell & molecular biology. Academic Press. Retrieved November 11, 2019 from http://ebookcentral.proquest.com/lib/lmu/detail.action?docID=311420.
# Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics. Jan 2009;25(2):288-289. Retrieved November 11, 2019 from http://amigo.geneontology.org/amigo/
# Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., ... & Fisk, D. G. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast. ''Nucleic Acids Research'', 40(D1), D700-D705.