LMU BioDB 2017 - User contributions [en]

Cwong34 Individual Statement

2017-12-16T04:26:15Z

Cwong34: Updated group report file name

=My statement=

[[Media:Individual_assessment_CW.docx|Corinne's individual assessment]]

=My wiki links=

[[Gene_hAPI]]

[[Gene_hAPI_Deliverables]]

[[Media:Gene_hAPI_Final_Presentation.pptx|Gene hAPI Final Presentation]]

[[Media:Cold_Shock_Yeast_Genome_Response.pdf|QA/DA Journal Club Presentation]]

[[Media:Gene_hAPI_Group_Report.pdf|Gene hAPI Group Report]]

Individual pages:
*[[Cwong34_Week_11|Cwong34 Week 11]]
*[[Cwong34_Week_12|Cwong34 Week 12]]
*[[Cwong34_Week_14|Cwong34 Week 14]]
*[[Cwong34_Week_15|Cwong34 Week 15]]

[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 20:51, 13 December 2017 (PST)

{{cwong34}}

Template:Gene hAPI

2017-12-15T05:32:14Z

Cwong34: /* Project Deliverables Checklist */ added check

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

=Project Manager=
[X]'''Milestone 1: Project “Scaffolding”'''

This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.

# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 12]], [[Week 14]], and [[Week 15]].
# Organize management tools for your team:
#* Workflow narratives
#* Action items
#* Testing results/reports
#** Bugs/feature requests
#** Question/answer sequences

[X]'''Milestone 2: Periodic Updates'''

Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.

# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructors will expect you to know and be able to report on the status of each member of your team at any time.
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.
# Monitor the status of the report-in-progress and other related documentation.
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.

=Data Analyst=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[X]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

=Quality Assurance=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[X]'''Milestone 3: Requirements Analysis'''

As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.

* The ''entire QA guild'' should become an expert on the information that can be retrieved for a gene, so that they know how IDs should look, how certain data types will be displayed, etc. This will help them detect flaws and areas of improvement as development work proceeds.
* ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.

[X]'''Milestone 4: On-going Testing of Respective Team Deliverables'''

The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
* ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).

=Coders=
[X]'''Milestone 0: Journal Club Presentation'''

* For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.

[X]'''Milestone 1: Working Environment Setup'''

Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
* Node.js 8.4.0 or newer
* Code-savvy editor such as Atom or Microsoft Visual Studio Code
* Web browser with developer tools (Seaver 120 uses Google Chrome)
* '''git''' version control software
* (depends on team) '''curl''' command

Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.

[X]'''Milestone 2: Version Control Setup'''

Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.

The Interaction and Integration team is responsible for this fork, and will do their own work on the ''master'' branch of this fork. Thus, many of the early steps in this procedure involve them, and they must accomplish these steps first before the others can proceed:

# All members of the Coder guild should acquire a GitHub account, if they don’t already have one (it’s free).
# One of the Coders of the Interaction and Integration team creates a fork of the GRNsight project.
# The Interaction and Integration team adds the GitHub accounts of all Coder guild members as ''collaborators'' on the fork.
# Once every team is a collaborator on this fork, they can then create their respective ''branches'' on the fork:
#* The Page Design team creates a branch called ''page-design''.
#* The Gene Database APIs team creates a branch called ''gene-database-apis''.
#* ''After'' the ''gene-database-apis'' branch is created, the JASPAR API team creates a branch '''from ''gene-database-apis''''' called ''jaspar-api''.

The teams will then do their work on their respective branches. The protocol for integrating your work is described in the ''Integration and Integration Testing'' milestone below.

The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.

[X]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''

Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
# '''git clone''' the GitHub fork created in the version control setup milestone on where you plan to work on the project.
# '''cd''' into the folder that contains the cloned repository
# '''git checkout''' the branch that is assigned to you:
#* Interaction and Integration: ''master'' (no need for an explicit checkout because the clone defaults to this branch)
#* Page Design: ''page-design''
#* Gene Database APIs: ''gene-database-apis''
#* JASPAR: ''jasper-api'' (note that as instructed above, '''this should be a branch of the ''gene-database-apis'' branch''')
# Follow the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.

[X]'''Milestone 4: Development, Implementation, and Localized Testing'''

At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:

* Page Design: ''web-client/public/html'' (this folder does not yet exist; you will need to create it) and ''web-client/test'' (in case you are able to write unit tests for your work)
** While running GRNsight, you will be able to access files in this folder through the URL http://localhost:5001/html/''filename''
* Gene Database APIs: ''web-client/public/js'' and ''web-client/test''
* JASPAR: ''web-client/public/js'' and ''web-client/test''
* Interaction and Integration: Because you are integrating the other teams’ work, you will likely interact with the entire ''web-client'' folder

For the Gene Database APIs and JASPAR teams, your work will not be visible to end-users until the first overall integration is done, so use ''unit tests'' as your initial approach for verifying that your code is working well. You will probably need to mock up your API calls so that you don’t bombard the web services with requests while unit testing. However, these sites are generally open access so you can probably write your ''initial'' set of tests using real requests and responses.

The Quality Assurance members of each team should take charge of manual testing. Specific suggested manual testing tasks are described in the [[Quality Assurance]] guild page.

The Interaction and Integration team should initially get to know the files being created and worked on by the other teams prior to the first integration milestone.

Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.

[[Category:Gene hAPI]]

[[Category:Group Projects]]

Template:Cwong34

2017-12-14T04:57:26Z

Cwong34: Added deliverables link

Cwong34 Week 15

2017-12-14T04:56:24Z

Cwong34: Added to electronic notebook

=Electronic Notebook=

*I created the Google document for the group report and formatted it.
*I checked in with the team members to see where we all are
*We scheduled a time to meet for us to work on the report together outside of class.
*I met with my group members over the weekend to work together on our report and PowerPoint.
*I met again with my group members during the week to finalize our presentation, and we worked more on the group report.
*We plan to meet again during the week to complete our report and check the rest of the deliverables before Friday.
*We met on Wednesday to finish up the report.
*I finished my [[Cwong34_Individual_Statement|individual statement]]

=Acknowledgments=
#I met up and worked with Dina, John, and Eddie A. on our project this week

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 18:43, 11 December 2017 (PST)

=References=
#LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{cwong34}}

[[Category: Journal Entry]]

Cwong34 Week 15

2017-12-14T04:55:03Z

Cwong34: Added to electronic notebook

=Electronic Notebook=

*I created the Google document for the group report and formatted it.
*I checked in with the team members to see where we all are
*We scheduled a time to meet for us to work on the report together outside of class.
*I met with my group members over the weekend to work together on our report and PowerPoint.
*I met again with my group members during the week to finalize our presentation, and we worked more on the group report.
*We plan to meet again during the week to complete our report and check the rest of the deliverables before Friday.
*We met on Wednesday to finish up the report.

=Acknowledgments=
#I met up and worked with Dina, John, and Eddie A. on our project this week

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 18:43, 11 December 2017 (PST)

=References=
#LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{cwong34}}

[[Category: Journal Entry]]

Cwong34 Individual Statement

2017-12-14T04:53:48Z

Cwong34: Added file

=My statement=

[[Media:Individual_assessment_CW.docx|Corinne's individual assessment]]

=My wiki links=

[[Gene_hAPI]]

[[Gene_hAPI_Deliverables]]

[[Media:Gene_hAPI_Final_Presentation.pptx|Gene hAPI Final Presentation]]

[[Media:Cold_Shock_Yeast_Genome_Response.pdf|QA/DA Journal Club Presentation]]

[[Media:…|Gene hAPI Group Report]]

Individual pages:
*[[Cwong34_Week_11|Cwong34 Week 11]]
*[[Cwong34_Week_12|Cwong34 Week 12]]
*[[Cwong34_Week_14|Cwong34 Week 14]]
*[[Cwong34_Week_15|Cwong34 Week 15]]

[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 20:51, 13 December 2017 (PST)

{{cwong34}}

File:Individual assessment CW.docx

2017-12-14T04:52:37Z

Cwong34: My individual statement

My individual statement

Cwong34 Individual Statement

2017-12-14T04:51:24Z

Cwong34: Added links to individual statement

=My statement=

...

=My wiki links=

[[Gene_hAPI]]

[[Gene_hAPI_Deliverables]]

[[Media:Gene_hAPI_Final_Presentation.pptx|Gene hAPI Final Presentation]]

[[Media:Cold_Shock_Yeast_Genome_Response.pdf|QA/DA Journal Club Presentation]]

[[Media:…|Gene hAPI Group Report]]

Individual pages:
*[[Cwong34_Week_11|Cwong34 Week 11]]
*[[Cwong34_Week_12|Cwong34 Week 12]]
*[[Cwong34_Week_14|Cwong34 Week 14]]
*[[Cwong34_Week_15|Cwong34 Week 15]]

[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 20:51, 13 December 2017 (PST)

{{cwong34}}

Gene hAPI Deliverables

2017-12-14T04:06:39Z

Cwong34: Added our pages

[[Gene hAPI]]

Members:
*[[User:Cazinge|Eddie Azinge]]
*[[User:Dbashour|Dina Bashoura]]
*[[User:Johnllopez616|John Lopez]]
*[[User:Cwong34|Corinne Wong]]

= Gene hAPI Deliverables =
# Organized team deliverables wiki page
#* [[Gene_hAPI_Deliverables|Gene hAPI Deliverables page (this current page)]]
# Group report
#*
# Individual statements
#* Eddie A.:
#* Dina:
#* John:
#* Corinne: [[Cwong34_Individual_Statement|Corinne's individual statement]]
# Group PowerPoint presentation
#* [[Media:Gene_hAPI_Final_Presentation.pptx | Gene hAPI final presentation]]
#* [[Media:JLopezEAzingeJournalClub.pptx | Coders' Journal Club Presentation]] 
#* [[Media:Cold_Shock_Yeast_Genome_Response.pdf | QA/Data Analyst Journal Club Presentation]]
# Code (GitHub pull request)
#*
# README
#*
# Excel spreadsheet with ANOVA results/stem formatting
#*
# PowerPoint of screenshots of stem results
#*
# Gene List and GO List files from each significant profile
#*
# YEASTRACT "rank by TF" results
#*
# GRNmap input workbook (with network adjency matrix)
#*
# GRNmap output workbook
#*
# Electronic notebooks
#* [[Dbashour_Week_8|Dina's Week 8]]
#* [[Dbashour_Week_10|Dina's Week 10]]
#* [[Dbashour_Week_11|Dina's Week 11]]
#* [[Dbashour_Week_12|Dina's Week 12]]
#* [[Dbashour_Week_14|Dina's Week 14]]
#* [[Dbashour_Week_15|Dina's Week 15]]

= Deliverables Checklist =

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

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

[[Category: Gene hAPI]]

[[Category: Group Project]]

[[Category: Deliverables]]

Gene hAPI Deliverables

2017-12-14T04:04:04Z

Cwong34: Added to deliverables

[[Gene hAPI]]

= Gene hAPI Deliverables =
# Organized team deliverables wiki page
#* [[Gene_hAPI_Deliverables|Gene hAPI Deliverables page (this current page)]]
# Group report
#*
# Individual statements
#* Eddie A.:
#* Dina:
#* John:
#* Corinne:[[Cwong34_Individual_Statement|Corinne's individual statement]]
# Group PowerPoint presentation
#* [[Media:Gene_hAPI_Final_Presentation.pptx | Gene hAPI final presentation]]
#* [[Media:JLopezEAzingeJournalClub.pptx | Coders' Journal Club Presentation]] 
#* [[Media:Cold_Shock_Yeast_Genome_Response.pdf | QA/Data Analyst Journal Club Presentation]]
# Code (GitHub pull request)
#*
# README
#*
# Excel spreadsheet with ANOVA results/stem formatting
#*
# PowerPoint of screenshots of stem results
#*
# Gene List and GO List files from each significant profile
#*
# YEASTRACT "rank by TF" results
#*
# GRNmap input workbook (with network adjency matrix)
#*
# GRNmap output workbook
#*
# Electronic notebooks
#* [[Dbashour_Week_8|Dina's Week 8]]
#* [[Dbashour_Week_10|Dina's Week 10]]
#* [[Dbashour_Week_11|Dina's Week 11]]
#* [[Dbashour_Week_12|Dina's Week 12]]
#* [[Dbashour_Week_14|Dina's Week 14]]
#* [[Dbashour_Week_15|Dina's Week 15]]

= Deliverables Checklist =

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

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

[[Category: Gene hAPI]]

[[Category: Group Project]]

[[Category: Deliverables]]

Gene hAPI Deliverables

2017-12-14T04:01:24Z

Cwong34: Added our user pages

[[Gene hAPI]]

Members:
*[[User:Cazinge|Eddie Azinge]]
*[[User:Dbashour|Dina Bashoura]]
*[[User:Johnllopez616|John Lopez]]
*[[User:Cwong34|Corinne Wong]]

= Gene hAPI Deliverables =
#[[Media:Gene_hAPI_Final_Presentation.pptx | Gene hAPI final presentation]]
#[[Media:JLopezEAzingeJournalClub.pptx | Coders' Journal Club Presentation]] 
#[[Media:Cold_Shock_Yeast_Genome_Response.pdf | QA/Data Analyst Journal Club Presentation]]

= Deliverables Checklist =

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

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

[[Category: Gene hAPI]]

[[Category: Group Project]]

[[Category: Deliverables]]

Gene hAPI Deliverables

2017-12-13T23:58:13Z

Cwong34: Added categories

[[Gene hAPI]]

= Gene hAPI Deliverables =
#[[Media:Gene_hAPI_Final_Presentation.pptx | Gene hAPI final presentation]]
#[[Media:JLopezEAzingeJournalClub.pptx | Coders' Journal Club Presentation]] 
#[[Media:Cold_Shock_Yeast_Genome_Response.pdf | QA/Data Analyst Journal Club Presentation]]

= Deliverables Checklist =

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

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

[[Category: Gene hAPI]]

[[Category: Group Project]]

[[Category: Deliverables]]

Gene hAPI Deliverables

2017-12-13T23:54:17Z

Cwong34: Changed format

Template:Gene hAPI

2017-12-13T23:53:22Z

Cwong34: Checked off some deliverables items

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

=Project Manager=
[X]'''Milestone 1: Project “Scaffolding”'''

This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.

# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 12]], [[Week 14]], and [[Week 15]].
# Organize management tools for your team:
#* Workflow narratives
#* Action items
#* Testing results/reports
#** Bugs/feature requests
#** Question/answer sequences

[X]'''Milestone 2: Periodic Updates'''

Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.

# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructors will expect you to know and be able to report on the status of each member of your team at any time.
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.
# Monitor the status of the report-in-progress and other related documentation.
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.

=Data Analyst=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[X]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

=Quality Assurance=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[X]'''Milestone 3: Requirements Analysis'''

As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.

* The ''entire QA guild'' should become an expert on the information that can be retrieved for a gene, so that they know how IDs should look, how certain data types will be displayed, etc. This will help them detect flaws and areas of improvement as development work proceeds.
* ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.

[X]'''Milestone 4: On-going Testing of Respective Team Deliverables'''

The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
* ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).

=Coders=
[X]'''Milestone 0: Journal Club Presentation'''

* For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.

[X]'''Milestone 1: Working Environment Setup'''

Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
* Node.js 8.4.0 or newer
* Code-savvy editor such as Atom or Microsoft Visual Studio Code
* Web browser with developer tools (Seaver 120 uses Google Chrome)
* '''git''' version control software
* (depends on team) '''curl''' command

Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.

[X]'''Milestone 2: Version Control Setup'''

Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.

The Interaction and Integration team is responsible for this fork, and will do their own work on the ''master'' branch of this fork. Thus, many of the early steps in this procedure involve them, and they must accomplish these steps first before the others can proceed:

# All members of the Coder guild should acquire a GitHub account, if they don’t already have one (it’s free).
# One of the Coders of the Interaction and Integration team creates a fork of the GRNsight project.
# The Interaction and Integration team adds the GitHub accounts of all Coder guild members as ''collaborators'' on the fork.
# Once every team is a collaborator on this fork, they can then create their respective ''branches'' on the fork:
#* The Page Design team creates a branch called ''page-design''.
#* The Gene Database APIs team creates a branch called ''gene-database-apis''.
#* ''After'' the ''gene-database-apis'' branch is created, the JASPAR API team creates a branch '''from ''gene-database-apis''''' called ''jaspar-api''.

The teams will then do their work on their respective branches. The protocol for integrating your work is described in the ''Integration and Integration Testing'' milestone below.

The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.

[X]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''

Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
# '''git clone''' the GitHub fork created in the version control setup milestone on where you plan to work on the project.
# '''cd''' into the folder that contains the cloned repository
# '''git checkout''' the branch that is assigned to you:
#* Interaction and Integration: ''master'' (no need for an explicit checkout because the clone defaults to this branch)
#* Page Design: ''page-design''
#* Gene Database APIs: ''gene-database-apis''
#* JASPAR: ''jasper-api'' (note that as instructed above, '''this should be a branch of the ''gene-database-apis'' branch''')
# Follow the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.

[X]'''Milestone 4: Development, Implementation, and Localized Testing'''

At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:

* Page Design: ''web-client/public/html'' (this folder does not yet exist; you will need to create it) and ''web-client/test'' (in case you are able to write unit tests for your work)
** While running GRNsight, you will be able to access files in this folder through the URL http://localhost:5001/html/''filename''
* Gene Database APIs: ''web-client/public/js'' and ''web-client/test''
* JASPAR: ''web-client/public/js'' and ''web-client/test''
* Interaction and Integration: Because you are integrating the other teams’ work, you will likely interact with the entire ''web-client'' folder

For the Gene Database APIs and JASPAR teams, your work will not be visible to end-users until the first overall integration is done, so use ''unit tests'' as your initial approach for verifying that your code is working well. You will probably need to mock up your API calls so that you don’t bombard the web services with requests while unit testing. However, these sites are generally open access so you can probably write your ''initial'' set of tests using real requests and responses.

The Quality Assurance members of each team should take charge of manual testing. Specific suggested manual testing tasks are described in the [[Quality Assurance]] guild page.

The Interaction and Integration team should initially get to know the files being created and worked on by the other teams prior to the first integration milestone.

Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.

[[Category:Gene hAPI]]

[[Category:Group Projects]]

Gene hAPI Deliverables

2017-12-13T23:52:55Z

Cwong34: Rearranged deliverables

[[Gene hAPI]]

= Gene hAPI Deliverables =
#[[Media:Gene_hAPI_Final_Presentation.pptx | Gene hAPI final presentation]]
#[[Media:JLopezEAzingeJournalClub.pptx | Coders' Journal Club Presentation]] 
#[[Media:Cold_Shock_Yeast_Genome_Response.pdf | QA/Data Analyst Journal Club Presentation]]

== Deliverables Checklist ==

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

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

Template:Gene hAPI

2017-12-12T02:55:22Z

Cwong34: Deleted Milestone 5 for coders

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

=Project Manager=
[X]'''Milestone 1: Project “Scaffolding”'''

This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.

# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 12]], [[Week 14]], and [[Week 15]].
# Organize management tools for your team:
#* Workflow narratives
#* Action items
#* Testing results/reports
#** Bugs/feature requests
#** Question/answer sequences

[X]'''Milestone 2: Periodic Updates'''

Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.

# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructors will expect you to know and be able to report on the status of each member of your team at any time.
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.
# Monitor the status of the report-in-progress and other related documentation.
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.

=Data Analyst=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[X]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

=Quality Assurance=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[X]'''Milestone 3: Requirements Analysis'''

As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.

* The ''entire QA guild'' should become an expert on the information that can be retrieved for a gene, so that they know how IDs should look, how certain data types will be displayed, etc. This will help them detect flaws and areas of improvement as development work proceeds.
* ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.

[X]'''Milestone 4: On-going Testing of Respective Team Deliverables'''

The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
* ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).

=Coders=
[X]'''Milestone 0: Journal Club Presentation'''

* For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.

[X]'''Milestone 1: Working Environment Setup'''

Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
* Node.js 8.4.0 or newer
* Code-savvy editor such as Atom or Microsoft Visual Studio Code
* Web browser with developer tools (Seaver 120 uses Google Chrome)
* '''git''' version control software
* (depends on team) '''curl''' command

Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.

[X]'''Milestone 2: Version Control Setup'''

Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.

The Interaction and Integration team is responsible for this fork, and will do their own work on the ''master'' branch of this fork. Thus, many of the early steps in this procedure involve them, and they must accomplish these steps first before the others can proceed:

# All members of the Coder guild should acquire a GitHub account, if they don’t already have one (it’s free).
# One of the Coders of the Interaction and Integration team creates a fork of the GRNsight project.
# The Interaction and Integration team adds the GitHub accounts of all Coder guild members as ''collaborators'' on the fork.
# Once every team is a collaborator on this fork, they can then create their respective ''branches'' on the fork:
#* The Page Design team creates a branch called ''page-design''.
#* The Gene Database APIs team creates a branch called ''gene-database-apis''.
#* ''After'' the ''gene-database-apis'' branch is created, the JASPAR API team creates a branch '''from ''gene-database-apis''''' called ''jaspar-api''.

The teams will then do their work on their respective branches. The protocol for integrating your work is described in the ''Integration and Integration Testing'' milestone below.

The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.

[X]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''

Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
# '''git clone''' the GitHub fork created in the version control setup milestone on where you plan to work on the project.
# '''cd''' into the folder that contains the cloned repository
# '''git checkout''' the branch that is assigned to you:
#* Interaction and Integration: ''master'' (no need for an explicit checkout because the clone defaults to this branch)
#* Page Design: ''page-design''
#* Gene Database APIs: ''gene-database-apis''
#* JASPAR: ''jasper-api'' (note that as instructed above, '''this should be a branch of the ''gene-database-apis'' branch''')
# Follow the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.

[X]'''Milestone 4: Development, Implementation, and Localized Testing'''

At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:

* Page Design: ''web-client/public/html'' (this folder does not yet exist; you will need to create it) and ''web-client/test'' (in case you are able to write unit tests for your work)
** While running GRNsight, you will be able to access files in this folder through the URL http://localhost:5001/html/''filename''
* Gene Database APIs: ''web-client/public/js'' and ''web-client/test''
* JASPAR: ''web-client/public/js'' and ''web-client/test''
* Interaction and Integration: Because you are integrating the other teams’ work, you will likely interact with the entire ''web-client'' folder

For the Gene Database APIs and JASPAR teams, your work will not be visible to end-users until the first overall integration is done, so use ''unit tests'' as your initial approach for verifying that your code is working well. You will probably need to mock up your API calls so that you don’t bombard the web services with requests while unit testing. However, these sites are generally open access so you can probably write your ''initial'' set of tests using real requests and responses.

The Quality Assurance members of each team should take charge of manual testing. Specific suggested manual testing tasks are described in the [[Quality Assurance]] guild page.

The Interaction and Integration team should initially get to know the files being created and worked on by the other teams prior to the first integration milestone.

Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.

[[Category:Gene hAPI]]

[[Category:Group Projects]]

Gene hAPI

2017-12-12T02:52:08Z

Cwong34: Added my week 15 section

==Gene hAPI==

===Links===
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

{{Template:GRNsight Gene Page Project Links}}

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
*[[Cazinge Week 14|Week 14]]:
**This week's we reached a good spot in terms of the execution of Milestone 4. I was the main point of contact with regards to general coding questions, and we're approaching the completion of the final assignment.
**This week was fun as I was able to leisurely interact with my classmates in an environment more typically representing that of actual software development. As such, I was able to help out with typical software development problems and speed up the development of the final project.
**I don't feel as if I struggled with any specific part of this week's assignment, but we haven't exactly been proactive about writing our tests, so that eventually needs to be resolved.
**As far as what needs to get done for this next week, testing. Other than that, I'm feeling good about our progress going into the last week.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)
*[[Cazinge Week 15|Week 15]]:
**This week we finished the final functionality of the API function, marking our progress with the final project complete.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)
*[[Dbashour_Week_14 | Week 14]]
** This week, I corrected my week 8 and week 10 assignments on my [[Dbashour_Week_14 | Week 14]] individual page., fixing anything that Dr. Dahlquist and Dr. Dionisio had requested to fix on my talk page. I made my electronic notebook be written in the past tense, corrected my files, and added any information I needed to add. Also this week I completed the remainder of the week 10 assignment that we had not complete during that week. I made a network model of transcription factors based on my deletion strain dGLN3. I also met with the data analysts to see if we were all on the same page and made a group message in order to have a method of communication for any questions we had.
** Being on top of my assignments and my time management during class worked well this week. I was able to ask questions and accomplish a lot from working on my assignment in class in a timely manner.
** I would have liked to meet more with my group and touch base on where we all resided in the project. I wish that we updated each other more on what we were working on, specifically between the coders and the analysts/QA.
** Next week, I hope to continue my efforts of time management in class and communicate more with the coders to see how far we have all come. I will specifically ask the coders what they have done and what they plan on doing next in order to facilitate the communication barrier. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)
*[[Dbashour_Week_15 | Week 15]]
** This week, Dr. Dahlquist reviewed my files and made corrections to them so that they would work and be visualized in GRNsight. I organized my final deliverables in order to prepare for the final project. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week 12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

*[[Cwong34_Week_14|Week 14]]:
**This week, I met with the group members to check in on where we were in the project. I met with the other QAs, and we worked together to come up with a list of information to pull from databases, and specifically which information to pull from where.
**Having time to work on the project in class was very helpful to be able to meet with everyone. I could easily communicate to my team members and check in with them, but I could also check in with other teams to work together. There was a lot more communication this week, and I feel I have a good idea of our progression for the rest of the semester.
**Having to split the class time between working with our team members and working with our guilds was a bit of a challenge because there was a lot to cover between both groups. We made it work, but hopefully we'll be able to find a time to meet outside of class as well this coming week to work on our project.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:25, 5 December 2017 (PST)

*[[Cwong34_Week_15|Week 15]]
**

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

=Acknowledgments=
#We received help and guidance from Dr. Dondi and Dr. Dahlquist.

=References=
#Becerra M., Lombardía L.J., González-Siso M.I., Rodríguez-Belmonte E., Hauser N.C., & Cerdán M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Paul Ford, 2015, Bloomberg, Retrieved from: https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
#Homma T., Iwahashi H., & Komatsu Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237. https://doi.org/10.1016/S0011-2240(03)00028-2
#LMU BioDB 2017. (2017). GRNsight Gene Page Project. Retrieved from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project
#Murata et. al.(2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

Gene hAPI

2017-12-12T02:49:11Z

Cwong34: Moved GRNsight Gene Page Project Links template

==Gene hAPI==

===Links===
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

{{Template:GRNsight Gene Page Project Links}}

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
*[[Cazinge Week 14|Week 14]]:
**This week's we reached a good spot in terms of the execution of Milestone 4. I was the main point of contact with regards to general coding questions, and we're approaching the completion of the final assignment.
**This week was fun as I was able to leisurely interact with my classmates in an environment more typically representing that of actual software development. As such, I was able to help out with typical software development problems and speed up the development of the final project.
**I don't feel as if I struggled with any specific part of this week's assignment, but we haven't exactly been proactive about writing our tests, so that eventually needs to be resolved.
**As far as what needs to get done for this next week, testing. Other than that, I'm feeling good about our progress going into the last week.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)
*[[Cazinge Week 15|Week 15]]:
**This week we finished the final functionality of the API function, marking our progress with the final project complete.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)
*[[Dbashour_Week_14 | Week 14]]
** This week, I corrected my week 8 and week 10 assignments on my [[Dbashour_Week_14 | Week 14]] individual page., fixing anything that Dr. Dahlquist and Dr. Dionisio had requested to fix on my talk page. I made my electronic notebook be written in the past tense, corrected my files, and added any information I needed to add. Also this week I completed the remainder of the week 10 assignment that we had not complete during that week. I made a network model of transcription factors based on my deletion strain dGLN3. I also met with the data analysts to see if we were all on the same page and made a group message in order to have a method of communication for any questions we had.
** Being on top of my assignments and my time management during class worked well this week. I was able to ask questions and accomplish a lot from working on my assignment in class in a timely manner.
** I would have liked to meet more with my group and touch base on where we all resided in the project. I wish that we updated each other more on what we were working on, specifically between the coders and the analysts/QA.
** Next week, I hope to continue my efforts of time management in class and communicate more with the coders to see how far we have all come. I will specifically ask the coders what they have done and what they plan on doing next in order to facilitate the communication barrier. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)
*[[Dbashour_Week_15 | Week 15]]
** This week, Dr. Dahlquist reviewed my files and made corrections to them so that they would work and be visualized in GRNsight. I organized my final deliverables in order to prepare for the final project. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week 12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

*[[Cwong34_Week_14|Week 14]]:
**This week, I met with the group members to check in on where we were in the project. I met with the other QAs, and we worked together to come up with a list of information to pull from databases, and specifically which information to pull from where.
**Having time to work on the project in class was very helpful to be able to meet with everyone. I could easily communicate to my team members and check in with them, but I could also check in with other teams to work together. There was a lot more communication this week, and I feel I have a good idea of our progression for the rest of the semester.
**Having to split the class time between working with our team members and working with our guilds was a bit of a challenge because there was a lot to cover between both groups. We made it work, but hopefully we'll be able to find a time to meet outside of class as well this coming week to work on our project.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:25, 5 December 2017 (PST)

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

=Acknowledgments=
#We received help and guidance from Dr. Dondi and Dr. Dahlquist.

=References=
#Becerra M., Lombardía L.J., González-Siso M.I., Rodríguez-Belmonte E., Hauser N.C., & Cerdán M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Paul Ford, 2015, Bloomberg, Retrieved from: https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
#Homma T., Iwahashi H., & Komatsu Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237. https://doi.org/10.1016/S0011-2240(03)00028-2
#LMU BioDB 2017. (2017). GRNsight Gene Page Project. Retrieved from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project
#Murata et. al.(2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

Gene hAPI

2017-12-12T02:47:54Z

Cwong34: Added important links

==Gene hAPI==

===Links===
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
*[[Cazinge Week 14|Week 14]]:
**This week's we reached a good spot in terms of the execution of Milestone 4. I was the main point of contact with regards to general coding questions, and we're approaching the completion of the final assignment.
**This week was fun as I was able to leisurely interact with my classmates in an environment more typically representing that of actual software development. As such, I was able to help out with typical software development problems and speed up the development of the final project.
**I don't feel as if I struggled with any specific part of this week's assignment, but we haven't exactly been proactive about writing our tests, so that eventually needs to be resolved.
**As far as what needs to get done for this next week, testing. Other than that, I'm feeling good about our progress going into the last week.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)
*[[Cazinge Week 15|Week 15]]:
**This week we finished the final functionality of the API function, marking our progress with the final project complete.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)
*[[Dbashour_Week_14 | Week 14]]
** This week, I corrected my week 8 and week 10 assignments on my [[Dbashour_Week_14 | Week 14]] individual page., fixing anything that Dr. Dahlquist and Dr. Dionisio had requested to fix on my talk page. I made my electronic notebook be written in the past tense, corrected my files, and added any information I needed to add. Also this week I completed the remainder of the week 10 assignment that we had not complete during that week. I made a network model of transcription factors based on my deletion strain dGLN3. I also met with the data analysts to see if we were all on the same page and made a group message in order to have a method of communication for any questions we had.
** Being on top of my assignments and my time management during class worked well this week. I was able to ask questions and accomplish a lot from working on my assignment in class in a timely manner.
** I would have liked to meet more with my group and touch base on where we all resided in the project. I wish that we updated each other more on what we were working on, specifically between the coders and the analysts/QA.
** Next week, I hope to continue my efforts of time management in class and communicate more with the coders to see how far we have all come. I will specifically ask the coders what they have done and what they plan on doing next in order to facilitate the communication barrier. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)
*[[Dbashour_Week_15 | Week 15]]
** This week, Dr. Dahlquist reviewed my files and made corrections to them so that they would work and be visualized in GRNsight. I organized my final deliverables in order to prepare for the final project. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week 12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

*[[Cwong34_Week_14|Week 14]]:
**This week, I met with the group members to check in on where we were in the project. I met with the other QAs, and we worked together to come up with a list of information to pull from databases, and specifically which information to pull from where.
**Having time to work on the project in class was very helpful to be able to meet with everyone. I could easily communicate to my team members and check in with them, but I could also check in with other teams to work together. There was a lot more communication this week, and I feel I have a good idea of our progression for the rest of the semester.
**Having to split the class time between working with our team members and working with our guilds was a bit of a challenge because there was a lot to cover between both groups. We made it work, but hopefully we'll be able to find a time to meet outside of class as well this coming week to work on our project.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:25, 5 December 2017 (PST)

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

=Acknowledgments=
#We received help and guidance from Dr. Dondi and Dr. Dahlquist.

=References=
#Becerra M., Lombardía L.J., González-Siso M.I., Rodríguez-Belmonte E., Hauser N.C., & Cerdán M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Paul Ford, 2015, Bloomberg, Retrieved from: https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
#Homma T., Iwahashi H., & Komatsu Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237. https://doi.org/10.1016/S0011-2240(03)00028-2
#LMU BioDB 2017. (2017). GRNsight Gene Page Project. Retrieved from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project
#Murata et. al.(2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

{{Template:GRNsight Gene Page Project Links}}

Template:Gene hAPI

2017-12-12T02:47:41Z

Cwong34: Removed links from template - added to actual page

Cwong34 Week 15

2017-12-12T02:43:04Z

Cwong34: Added to electronic notebook

=Electronic Notebook=

*I created the Google document for the group report and formatted it.
*I checked in with the team members to see where we all are
*We scheduled a time to meet for us to work on the report together outside of class.
*I met with my group members over the weekend to work together on our report and PowerPoint.
*I met again with my group members during the week to finalize our presentation, and we worked more on the group report.
*We plan to meet again during the week to complete our report and check the rest of the deliverables before Friday.

=Acknowledgments=
#I met up and worked with Dina, John, and Eddie A. on our project this week

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 18:43, 11 December 2017 (PST)

=References=
#LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{cwong34}}

[[Category: Journal Entry]]

Gene hAPI

2017-12-09T21:01:22Z

Cwong34: Added reference and acknowledgment

==Gene hAPI==

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
*[[Cazinge Week 14|Week 14]]:
**This week's we reached a good spot in terms of the execution of Milestone 4. I was the main point of contact with regards to general coding questions, and we're approaching the completion of the final assignment.
**This week was fun as I was able to leisurely interact with my classmates in an environment more typically representing that of actual software development. As such, I was able to help out with typical software development problems and speed up the development of the final project.
**I don't feel as if I struggled with any specific part of this week's assignment, but we haven't exactly been proactive about writing our tests, so that eventually needs to be resolved.
**As far as what needs to get done for this next week, testing. Other than that, I'm feeling good about our progress going into the last week.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)
*[[Cazinge Week 15|Week 15]]:
**This week we finished the final functionality of the API function, marking our progress with the final project complete.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)
*[[Dbashour_Week_14 | Week 14]]
** This week, I corrected my week 8 and week 10 assignments on my [[Dbashour_Week_14 | Week 14]] individual page., fixing anything that Dr. Dahlquist and Dr. Dionisio had requested to fix on my talk page. I made my electronic notebook be written in the past tense, corrected my files, and added any information I needed to add. Also this week I completed the remainder of the week 10 assignment that we had not complete during that week. I made a network model of transcription factors based on my deletion strain dGLN3. I also met with the data analysts to see if we were all on the same page and made a group message in order to have a method of communication for any questions we had.
** Being on top of my assignments and my time management during class worked well this week. I was able to ask questions and accomplish a lot from working on my assignment in class in a timely manner.
** I would have liked to meet more with my group and touch base on where we all resided in the project. I wish that we updated each other more on what we were working on, specifically between the coders and the analysts/QA.
** Next week, I hope to continue my efforts of time management in class and communicate more with the coders to see how far we have all come. I will specifically ask the coders what they have done and what they plan on doing next in order to facilitate the communication barrier. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)
*[[Dbashour_Week_15 | Week 15]]
** This week, Dr. Dahlquist reviewed my files and made corrections to them so that they would work and be visualized in GRNsight. I organized my final deliverables in order to prepare for the final project. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 13:00, 9 December 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week 12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

*[[Cwong34_Week_14|Week 14]]:
**This week, I met with the group members to check in on where we were in the project. I met with the other QAs, and we worked together to come up with a list of information to pull from databases, and specifically which information to pull from where.
**Having time to work on the project in class was very helpful to be able to meet with everyone. I could easily communicate to my team members and check in with them, but I could also check in with other teams to work together. There was a lot more communication this week, and I feel I have a good idea of our progression for the rest of the semester.
**Having to split the class time between working with our team members and working with our guilds was a bit of a challenge because there was a lot to cover between both groups. We made it work, but hopefully we'll be able to find a time to meet outside of class as well this coming week to work on our project.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:25, 5 December 2017 (PST)

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

=Acknowledgments=
#We received help and guidance from Dr. Dondi and Dr. Dahlquist.

=References=
#Becerra M., Lombardía L.J., González-Siso M.I., Rodríguez-Belmonte E., Hauser N.C., & Cerdán M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Paul Ford, 2015, Bloomberg, Retrieved from: https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
#Homma T., Iwahashi H., & Komatsu Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237. https://doi.org/10.1016/S0011-2240(03)00028-2
#LMU BioDB 2017. (2017). GRNsight Gene Page Project. Retrieved from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project
#Murata et. al.(2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

{{Template:GRNsight Gene Page Project Links}}

Gene hAPI

2017-12-09T20:58:34Z

Cwong34: Added references

==Gene hAPI==

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
*[[Cazinge Week 14|Week 14]]:
**This week's we reached a good spot in terms of the execution of Milestone 4. I was the main point of contact with regards to general coding questions, and we're approaching the completion of the final assignment.
**This week was fun as I was able to leisurely interact with my classmates in an environment more typically representing that of actual software development. As such, I was able to help out with typical software development problems and speed up the development of the final project.
**I don't feel as if I struggled with any specific part of this week's assignment, but we haven't exactly been proactive about writing our tests, so that eventually needs to be resolved.
**As far as what needs to get done for this next week, testing. Other than that, I'm feeling good about our progress going into the last week.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)
*[[Cazinge Week 15|Week 15]]:
**This week we finished the final functionality of the API function, marking our progress with the final project complete.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 13:18, 8 December 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week 12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

*[[Cwong34_Week_14|Week 14]]:
**This week, I met with the group members to check in on where we were in the project. I met with the other QAs, and we worked together to come up with a list of information to pull from databases, and specifically which information to pull from where.
**Having time to work on the project in class was very helpful to be able to meet with everyone. I could easily communicate to my team members and check in with them, but I could also check in with other teams to work together. There was a lot more communication this week, and I feel I have a good idea of our progression for the rest of the semester.
**Having to split the class time between working with our team members and working with our guilds was a bit of a challenge because there was a lot to cover between both groups. We made it work, but hopefully we'll be able to find a time to meet outside of class as well this coming week to work on our project.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:25, 5 December 2017 (PST)

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

=Acknowledgments=

=References=
#Becerra M., Lombardía L.J., González-Siso M.I., Rodríguez-Belmonte E., Hauser N.C., & Cerdán M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Paul Ford, 2015, Bloomberg, Retrieved from: https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting
#Homma T., Iwahashi H., & Komatsu Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237. https://doi.org/10.1016/S0011-2240(03)00028-2
#LMU
#Murata et. al.(2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

{{Template:GRNsight Gene Page Project Links}}

Gene hAPI Deliverables

2017-12-07T23:52:31Z

Cwong34: Added updated format of report

== Deliverables Checklist ==

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

=Group Report Update=
*1-2 page introduction
*Methods
**Data analyst
**QA
**Coders
*Combine results/discussion - add few sentences about significance after each result
**DA
**QA
**Coders
*Conclusion 1-2 pages
**Connect to JC papers
**Future direction
**Summary

== Our Deliverables ==
#[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
#[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

Cwong34 Week 15

2017-12-06T00:57:19Z

Cwong34: Added electronic notebook, category, acknowledgments, references

=Electronic Notebook=

*I created the Google document for the group report and formatted it.
*I checked in with the team members to see where we all are
*We scheduled a time to meet for us to work on the report together outside of class.

=Acknowledgments=
#I met up and worked with Dina, John, and Eddie A. on our project this week

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

=References=
#LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

[[Category: Journal Entry]]

Template:Cwong34

2017-12-06T00:52:40Z

Cwong34: Added week 15

Gene hAPI

2017-12-05T08:25:15Z

Cwong34: Added week 14 summary

==Gene hAPI==

===General Information===
Eddie (Cazinge):
*Role: Coder
*User Page: [[User:cazinge|Eddie Azinge]]

Dina (Dbashour):
*Role: Data Analysis
*User Page: [[User:dbashour|Dina Bashoura]]

Corinne (Cwong34):
*Role: Project Manager/Quality Assurance
*User Page: [[User:Cwong34|Corinne Wong]]

John (johnllopez616):
*Role: Coder
*User Page: [[User:johnllopez616|John Lopez]]

===Executive Summaries===
'''Eddie''':
* [[Cazinge Week 11|Week 11]]:
** This week, I finished the bulk of the function logic for our final project; I also performed research on the items necessary for an effective journal club presentation this coming Thursday by completing the individual assignment that we were assigned for the week.
** Getting a large portion of our designated assignment completed early worked pretty successfully to alleviate our stress over the impending assignment and place us ahead of the pace of other groups so that we would be able to work on the more secondary parts of our final presentation across the next 4 weeks.
** Working on the project without having a proper development environment set up ended up detracting from the fluidity of our collaboration as a team; as the versions of the final function that John and I worked on weren't linked via git, and were somewhat unruly to collaborate on.
** Next time, I'll make sure to set up my development environment according to Dondi's instructions on the Coders Guild Page.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)
* [[Cazinge Week 12|Week 12]]:
** This week my task was to set up my development environment for the coder milestones. As such, I've completed milestones 1-3, talked to the other coders, and established a plan to work on the assignment in the future along with the rest of my team.
** Setting up milestones 1-3 went pretty well; since they were all standard open source project tasks, I was able to complete them simply, efficiently, and without any real friction.
** The only thing that I found less than desirable from this week was our communication; As Thanksgiving weekend rolls around we only stand to fall behind if we continue without amending our communication situation.
** This next week, I'll focus on keeping an open line of communication with the rest of my team, as well as completing the majority of the coding milestones that we have left.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 23:39, 20 November 2017 (PST)

'''Dina''':
* [[Dbashour_Week_11 | Week 11]]
** For this week, I assisted with creating our group wiki page, adding the template and setting up the page in preparation for the later weeks to come. I also located two out of 4 research articles regarding cold shock, yeast, and microarray data that we might later use for our final project. I became familiar with how to narrow down search queries in order to yield the smallest amount of results that are related to your actual topic, as well as identify how many articles are cited and how many articles cite the articles I found.
** I liked being able to work on the assignment in class, this way I was able to ask questions or clarify certain things that I needed help with. I also like that we have a guild of people, this way there is more of a support system if I am ever lost or need assistance.
** Because my task for this week was simply following the directions on the wiki, there was nothing that went wrong or needed fixing.
** Next week, I will work with my guild to present on our found articles and collaborate with them all in order to make our presentation run smoothly. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 23:43, 13 November 2017 (PST)
*[[Dbashour_Week_12 | Week 12]]
** For this week, Corrine and I prepared for the journal club presentation by individually reading the article "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. After reading this article, I developed an outline that highlighted the main points in each section of the article. With Corrine, I made a presentation on that outline, making sure to include each highlighted point. I also located and defined 10 words in the article that I was unfamiliar with and presented a flowchart of the overall experimental design.
** What worked well for this week was to collaborate with Corrine on who was going to present which parts of the article, this way there was no confusion on that matter and the overall flow of the presentation would be well executed.
** There was a lack of communication with all of us as a team, so I am unsure as to what John and Eddie have done for this week.
** Next week, we will all communicate via text either with the entire class or with just my group in order to clarify what the role of each person is and if we have been completing our tasks. 
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 12:10, 21 November 2017 (PST)

'''Corinne''':
* [[Cwong34_Week_11|Week 11]]:
** This week I helped to create the template and group page. I found two sources to contribute to our annotated bibliography, which we can use to research information for our final project. I researched the accessibility and publishing details of the sources.
** It was nice that we had some time in class to work, so we could easily check in with each other about what we were working on. It was also nice that Dina and I were working on the same project, so we could easily understand our work and help each other.
** It was a bit difficult to be fully aware of the progress of everyone because we had separate projects for this week and next week too. Both halves of our group are working on separate presentations, so we have different focuses, which makes it harder to keep up with each other.
** Next week, since it will be a similar situation, I will try to keep up with the other half of my group by fully understanding their objectives/assignments for the week and checking in some more.
*[[Cwong34_Week_12|Week 12]]:
**This week, I read the "Comprehensive expression analysis of time-dependent responses in yeast cells to low temperature" by Sahara, T., Goda, T., & Ohgiya, S. I came up with a flow chart of their methods for the experiment and made an outline for my individual assignment. I also found ten terms I didn't know and wrote down their definitions in my individual journal. I worked with Dina on our presentation of the article over the weekend.
**Having a collaborative assignment worked for me and Dina because we knew exactly what we needed to do for the project this week, and we worked together to get it done. Moreover, we had more time to meet up with each other this weekend, so it was easier to collaborate.
**It was still difficult to keep in touch with all of the members of the group since we all had different things to work on.
**However, now that we are done with our separate presentations, it will be more of a focus to know what each person is working on. Moreover, I will work to create more communication between group members to keep track of our progress, whether it's on our gene page or over text.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 23:26, 20 November 2017 (PST)

*[[Cwong34_Week_14|Week 14]]:
**This week, I met with the group members to check in on where we were in the project. I met with the other QAs, and we worked together to come up with a list of information to pull from databases, and specifically which information to pull from where.
**Having time to work on the project in class was very helpful to be able to meet with everyone. I could easily communicate to my team members and check in with them, but I could also check in with other teams to work together. There was a lot more communication this week, and I feel I have a good idea of our progression for the rest of the semester.
**Having to split the class time between working with our team members and working with our guilds was a bit of a challenge because there was a lot to cover between both groups. We made it work, but hopefully we'll be able to find a time to meet outside of class as well this coming week to work on our project.
[[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:25, 5 December 2017 (PST)

'''John''':
* [[Johnllopez Week 11|Week 11]]:
** This week my task was mostly focused around organizing the Journal Club Presentation. I created the initial outline for the powerpoint, created the style, and added over half the content to it. In addition, I spent some time with [[User:cazinge | Eddie Azinge]] who finished most of the deliverable portion of the assignment as he explained to me his process.
** I felt the assembling of the group was done so with ease because I worked with each of the people in the past on different assignments/projects. I felt like each of my members are dedicated and willing to work, so I'm glad that we have a good group. Eddie's experience in coding was an advantage for me because I shouldn't have any sort of confusion, however as I explain below, it is also a disadvantage.
** Despite the fact that Eddie provided an explanation for how he was able to develop the primary deliverable for the project, I felt a little disappointed that I couldn't go through the same discovery process he did. It essentially makes me feel like my role in the project isn't as important. In addition, I was also irritated that we didn't have many opportunities to work on the Journal Club Presentations in advance, for I felt like we weren't as prepared to create/give them as we could have been.
**Next week, I know that I have to get a head start on my individual portion of the assignment so that I'm not crunched for time like I was for the presentation. In addition, it's imperative that I review the code Eddie set up in detail so I can understand each line and how it works. Furthermore, I have to follow along with the other coders in setting up development rigs.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:41, 13 November 2017 (PST)

* [[Johnllopez Week 12|Week 12]]:
** This week my task involved setting up my development environment for the later milestones. It included the establishment of milestones 1-3, talking to the other coders, and establishing a plan to work on the assignment in the future.
** I felt like the setting up of the environment went well. Once I understood what I had to do, it was not difficult to set up the environment. In addition, I had no problems setting it up on GitHub and my computer once it happened.
** Unfortunately I felt like this week wasn't a very productive week. Despite setting up the environment, I did not collaborate well with my teammates. We have yet to arrange a proper work schedule and plan, especially to ensure that over the thanksgiving break we are able to do some stuff. This has led to the group's progress existing in a state of limbo.
** On Thursday, I asked the class to obtain a WhatsApp to allow for communication. This will be essential to communicate between the coders to accomplish the project. On Tuesday I will connect with as many people in the class. More importantly, I will get my group together to work on a set plan to work on the assignment and establish deadlines. Although this week wasn't the most productive for me, I will ensure that we don't fall behind next week.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:27, 20 November 2017 (PST)

*[[johnllopez Week 14|Week 14]]:
**This week's primary objective was to get as much of Milestone 4 as finished as possible. My portion of the assignment was to learn how to extract data from XML files and translate it so that the page developers could use it.
**Perhaps the best part about this portion of the assignment was being able to discover a bit of jQuery and DOM functions. Knowledge and exposure to both of these is fundamental in obtaining a potential job.
**One area where I struggled was figuring out how to extract JSON using javascript. This is something that both of the Eddies, however, were proficient in doing, so it's important that I seek their help in understanding this concept. In addition, I wish I communicated more with the coders during the development of the project.
**This week will be crucial in finishing Milestone 4 for the project. It's absolutely necessary that the coders and I not only integrate everything, but that I am following along with what they do. I will ask a lot of questions to truly understand what's happening.
[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:16, 4 December 2017 (PST)

==Journal Club Deliverable==
[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

== Journal Club Article ==
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
 
{{template:Gene_hAPI}}

Cwong34 Week 14

2017-12-05T08:15:45Z

Cwong34: Added acknowledgment and signature

=Gene Database Information=
The QA's met, and we chose which information we wanted to take from which databases.

'''NCBI'''
*Locus tag
**YGL073W
*Gene ID
**852806
*Also known as
**EXA3; MAS3

'''UniProt'''
*Protein type/name
**Heat shock factor protein
*Species
**''Saccharomyces cerevisiae'' (strain ATCC 204508 / S288c) (Baker's yeast)
*Protein sequence
**MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK
*Gene ID
**P10961 (HSF_YEAST)
*Similar proteins & ID of similar protein
**N1P1W2 - ID: P10961

'''Ensembl'''
*DNA sequence
**>chromosome:R64-1-1:VII:368153:371854:1
AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA
ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA
TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT
CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA
GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA
TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG
CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT
TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA
ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG
AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC
ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT
ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT
ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT
ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC
CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA
ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA
TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA
CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC
CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG
AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT
TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT
TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT
GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC
TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT
AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC
AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC
AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT
AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA
ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG
ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG
ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA
GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC
ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC
AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC
ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC
AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC
AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA
AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA
TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG
GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT
CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC
AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA
GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT
AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC
AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC
AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT
GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA
ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT
ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC
CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT
AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA
GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT
TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA
GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT
TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT
AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA
AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC
TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA
GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG
GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT
CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT
CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC
*Gene description/function
**Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]
*Gene ID
**YGL073W
*Gene map
**[[Image:Saccharomycescerevisiae_HSF1.pdf]]
*Gene location
**Chromosome VII: 368,753-371,254

'''SGD'''
*Gene ID
**S000003041
*Standard name
**HSF1
*Systematic name YGL073W
*Gene regulation (Regulators & targets)
**Regulators: 6
**Targets: 478
*Total interactions
**85 total for 71 unique genes
*Physical interactions
**Affinity Capture-MS: 11
**Affinity Capture-RNA: 1
**Affinity Capture-Western: 4
**Biochemical Activity: 11
**Co-localization: 3
**Reconstituted Complex: 2
**Two-hybrid: 3
*Genetic interactions
**Dosage Rescue: 16
**Negative Genetic: 8
**Phenotypic Suppression: 5
**Synthetic Growth Defect: 2
**Synthetic Haploinsufficiency: 1
**Synthetic Lethality: 6
**Synthetic Rescue: 11
*Gene ontology
**Summary: Sequence-specific DNA binding transcription factor that induces expression of the Hsp90-family protein chaperones Hsc82p and Hsp82p during the cellular response to heat; also negatively regulates TOR signaling
**Molecular Function:
***Manually Curated: DNA binding transcription factor activity (IDA)
***High-Throughput: sequence-specific DNA binding (HDA)
**Biological Process
***Manually Curated: negative regulation of TOR signaling (IMP), positive regulation of transcription from RNA polymerase II promoter (IMP), regulation of establishment of protein localization to chromosome (IMP), regulation of transcription from RNA polymerase II promoter (IDA), response to heat (IMP)
**Cellular Component
***Manually Curated: nucleus (IDA)
**High-Throughput: mitochondrion (HDA)

'''JASPAR'''
*Matrix ID
**MA0319.1
*Class
**Heat shock factors
*Sequence logo
**Image below
*Frequency matrix
**Image below
[[File:Jasper seq log and freq matrix.png]]

=Getting Organized=
*During class, I worked on our team page to map out our deliverables and milestones. I met with our team members to check in on how they are doing and to get a better idea of where our team is in our project.
*I created the deliverables page for our team ([[Gene hAPI Deliverables]])

=Acknowledgments=
#I worked with the other QAs and Dr. Dahlquist to come up with a list of information to pull from the different databases.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 00:15, 5 December 2017 (PST)

=References=
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{cwong34}}

[[Category: Journal Entry]]

Cwong34 Week 14

2017-12-03T00:02:44Z

Cwong34: Added to electronic notebook

=Gene Database Information=
The QA's met, and we chose which information we wanted to take from which databases.

'''NCBI'''
*Locus tag
**YGL073W
*Gene ID
**852806
*Also known as
**EXA3; MAS3

'''UniProt'''
*Protein type/name
**Heat shock factor protein
*Species
**''Saccharomyces cerevisiae'' (strain ATCC 204508 / S288c) (Baker's yeast)
*Protein sequence
**MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK
*Gene ID
**P10961 (HSF_YEAST)
*Similar proteins & ID of similar protein
**N1P1W2 - ID: P10961

'''Ensembl'''
*DNA sequence
**>chromosome:R64-1-1:VII:368153:371854:1
AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA
ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA
TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT
CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA
GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA
TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG
CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT
TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA
ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG
AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC
ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT
ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT
ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT
ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC
CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA
ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA
TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA
CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC
CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG
AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT
TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT
TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT
GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC
TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT
AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC
AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC
AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT
AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA
ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG
ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG
ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA
GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC
ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC
AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC
ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC
AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC
AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA
AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA
TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG
GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT
CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC
AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA
GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT
AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC
AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC
AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT
GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA
ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT
ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC
CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT
AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA
GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT
TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA
GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT
TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT
AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA
AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC
TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA
GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG
GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT
CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT
CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC
*Gene description/function
**Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]
*Gene ID
**YGL073W
*Gene map
**[[Image:Saccharomycescerevisiae_HSF1.pdf]]
*Gene location
**Chromosome VII: 368,753-371,254

'''SGD'''
*Gene ID
**S000003041
*Standard name
**HSF1
*Systematic name YGL073W
*Gene regulation (Regulators & targets)
**Regulators: 6
**Targets: 478
*Total interactions
**85 total for 71 unique genes
*Physical interactions
**Affinity Capture-MS: 11
**Affinity Capture-RNA: 1
**Affinity Capture-Western: 4
**Biochemical Activity: 11
**Co-localization: 3
**Reconstituted Complex: 2
**Two-hybrid: 3
*Genetic interactions
**Dosage Rescue: 16
**Negative Genetic: 8
**Phenotypic Suppression: 5
**Synthetic Growth Defect: 2
**Synthetic Haploinsufficiency: 1
**Synthetic Lethality: 6
**Synthetic Rescue: 11
*Gene ontology
**Summary: Sequence-specific DNA binding transcription factor that induces expression of the Hsp90-family protein chaperones Hsc82p and Hsp82p during the cellular response to heat; also negatively regulates TOR signaling
**Molecular Function:
***Manually Curated: DNA binding transcription factor activity (IDA)
***High-Throughput: sequence-specific DNA binding (HDA)
**Biological Process
***Manually Curated: negative regulation of TOR signaling (IMP), positive regulation of transcription from RNA polymerase II promoter (IMP), regulation of establishment of protein localization to chromosome (IMP), regulation of transcription from RNA polymerase II promoter (IDA), response to heat (IMP)
**Cellular Component
***Manually Curated: nucleus (IDA)
**High-Throughput: mitochondrion (HDA)

'''JASPAR'''
*Matrix ID
**MA0319.1
*Class
**Heat shock factors
*Sequence logo
**Image below
*Frequency matrix
**Image below
[[File:Jasper seq log and freq matrix.png]]

=Getting Organized=
*During class, I worked on our team page to map out our deliverables and milestones. I met with our team members to check in on how they are doing and to get a better idea of where our team is in our project.
*I created the deliverables page for our team ([[Gene hAPI Deliverables]])

=Acknowledgments=

=References=
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{cwong34}}

[[Category: Journal Entry]]

Cwong34 Week 14

2017-11-30T23:52:17Z

Cwong34: Added to database info list

=Gene Database Information=
The QA's met, and we chose which information we wanted to take from which databases.

'''NCBI'''
*Locus tag
**YGL073W
*Gene ID
**852806
*Also known as
**EXA3; MAS3

'''UniProt'''
*Protein type/name
*Protein sequence
*Gene ID
*Similar proteins

'''Ensembl'''
*DNA sequence
**>chromosome:R64-1-1:VII:368153:371854:1
AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA
ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA
TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT
CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA
GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA
TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG
CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT
TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA
ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG
AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC
ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT
ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT
ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT
ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC
CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA
ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA
TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA
CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC
CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG
AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT
TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT
TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT
GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC
TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT
AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC
AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC
AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT
AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA
ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG
ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG
ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA
GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC
ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC
AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC
ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC
AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC
AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA
AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA
TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG
GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT
CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC
AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA
GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT
AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC
AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC
AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT
GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA
ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT
ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC
CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT
AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA
GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT
TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA
GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT
TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT
AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA
AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC
TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA
GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG
GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT
CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT
CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC
*Gene description/function
**Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]
*Gene ID
**YGL073W
*Gene map
**[[Image:Saccharomycescerevisiae_HSF1.pdf]]
*Gene location
**Chromosome VII: 368,753-371,254

'''SGD'''
*Gene ID
*Gene regulation
*Gene ontology

'''JASPAR'''
*Gene ID
*Sequence logo
*Frequency matrix

=Getting Organized=
*During class, I worked on our team page to map out our deliverables and milestones. I met with our team members to check in on how they are doing and to get a better idea of where our team is in our project.
*I created the deliverables page for our team ([[Gene hAPI Deliverables]])

=Acknowledgments=

=References=
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{cwong34}}

[[Category: Journal Entry]]

File:Saccharomycescerevisiae HSF1.pdf

2017-11-30T23:48:18Z

Cwong34: Gene map of HSF1 and closely placed genes from Ensembl

Gene map of HSF1 and closely placed genes from Ensembl

Template:Gene hAPI

2017-11-30T23:37:18Z

Cwong34: Deleted milestones related to other team groups

= Gene hAPI Helpful Links =
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

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

=Project Manager=
[ ]'''Milestone 1: Project “Scaffolding”'''

This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.

# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 12]], [[Week 14]], and [[Week 15]].
# Organize management tools for your team:
#* Workflow narratives
#* Action items
#* Testing results/reports
#** Bugs/feature requests
#** Question/answer sequences

[ ]'''Milestone 2: Periodic Updates'''

Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.

# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructors will expect you to know and be able to report on the status of each member of your team at any time.
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.
# Monitor the status of the report-in-progress and other related documentation.
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.

=Data Analyst=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[ ]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

=Quality Assurance=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[ ]'''Milestone 3: Requirements Analysis'''

As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.

* The ''entire QA guild'' should become an expert on the information that can be retrieved for a gene, so that they know how IDs should look, how certain data types will be displayed, etc. This will help them detect flaws and areas of improvement as development work proceeds.
* ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.

[ ]'''Milestone 4: On-going Testing of Respective Team Deliverables'''

The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
* ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).

=Coders=
[X]'''Milestone 0: Journal Club Presentation'''

* For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.

[ ]'''Milestone 1: Working Environment Setup'''

Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
* Node.js 8.4.0 or newer
* Code-savvy editor such as Atom or Microsoft Visual Studio Code
* Web browser with developer tools (Seaver 120 uses Google Chrome)
* '''git''' version control software
* (depends on team) '''curl''' command

Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.

[ ]'''Milestone 2: Version Control Setup'''

Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.

The Interaction and Integration team is responsible for this fork, and will do their own work on the ''master'' branch of this fork. Thus, many of the early steps in this procedure involve them, and they must accomplish these steps first before the others can proceed:

# All members of the Coder guild should acquire a GitHub account, if they don’t already have one (it’s free).
# One of the Coders of the Interaction and Integration team creates a fork of the GRNsight project.
# The Interaction and Integration team adds the GitHub accounts of all Coder guild members as ''collaborators'' on the fork.
# Once every team is a collaborator on this fork, they can then create their respective ''branches'' on the fork:
#* The Page Design team creates a branch called ''page-design''.
#* The Gene Database APIs team creates a branch called ''gene-database-apis''.
#* ''After'' the ''gene-database-apis'' branch is created, the JASPAR API team creates a branch '''from ''gene-database-apis''''' called ''jaspar-api''.

The teams will then do their work on their respective branches. The protocol for integrating your work is described in the ''Integration and Integration Testing'' milestone below.

The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.

[ ]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''

Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
# '''git clone''' the GitHub fork created in the version control setup milestone on where you plan to work on the project.
# '''cd''' into the folder that contains the cloned repository
# '''git checkout''' the branch that is assigned to you:
#* Interaction and Integration: ''master'' (no need for an explicit checkout because the clone defaults to this branch)
#* Page Design: ''page-design''
#* Gene Database APIs: ''gene-database-apis''
#* JASPAR: ''jasper-api'' (note that as instructed above, '''this should be a branch of the ''gene-database-apis'' branch''')
# Follow the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.

[ ]'''Milestone 4: Development, Implementation, and Localized Testing'''

At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:

* Page Design: ''web-client/public/html'' (this folder does not yet exist; you will need to create it) and ''web-client/test'' (in case you are able to write unit tests for your work)
** While running GRNsight, you will be able to access files in this folder through the URL http://localhost:5001/html/''filename''
* Gene Database APIs: ''web-client/public/js'' and ''web-client/test''
* JASPAR: ''web-client/public/js'' and ''web-client/test''
* Interaction and Integration: Because you are integrating the other teams’ work, you will likely interact with the entire ''web-client'' folder

For the Gene Database APIs and JASPAR teams, your work will not be visible to end-users until the first overall integration is done, so use ''unit tests'' as your initial approach for verifying that your code is working well. You will probably need to mock up your API calls so that you don’t bombard the web services with requests while unit testing. However, these sites are generally open access so you can probably write your ''initial'' set of tests using real requests and responses.

The Quality Assurance members of each team should take charge of manual testing. Specific suggested manual testing tasks are described in the [[Quality Assurance]] guild page.

The Interaction and Integration team should initially get to know the files being created and worked on by the other teams prior to the first integration milestone.

Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.

[ ]'''Milestone 5: Integration and Integration Testing'''

Integration and integration testing should take place periodically to make sure that the overall gene page project is coming together well. Most of the Coders’ work for the remainder of the semester will be a cycle of the development and integration milestones. The Interaction and Integration team is in charge of coordinating when these integrations take place. The first integration will likely be the most difficult one to perform, but it is hoped that later iterations will proceed more smoothly.

When the other teams have reached the following sub-milestones, the first integration cycle can take place. Future iterations are at the discretion of the Interaction and Integration team in coordination with how the other teams are progressing:
* Page Design: first working version of the gene page
* Gene Database APIs: first working version of the <code>getGeneInformation</code> function
* JASPAR: This team’s work does not have to participate in the first integration cycle; instead, they should integrate their work with the Gene Database APIs team whenever they have a working prototype. JASPAR functionality simply “shows up” at some future integration cycle.
* Interaction and Integration: You are not blocked from working prior to the first integration; you can work on exploring the existing GRNsight code to implement the right-click functionality that will open the gene page in a new tab or window. You can start by making this code open a blank page. Upon the first integration iteration, you can then connect that page to the gene page provided by the Page Design team.

An individual integration iteration proceeds in this way:
# The Page Design and Gene Database APIs teams issue ''pull requests'' to merge their branches with the ''master'' branch.
# The Coders guild reviews each other’s code and points out any needed revisions.
# Once all revision requests are fulfilled, the Interaction and Integration team merges the pull requests into ''master''.
# The Coders guild resolves any merge conflicts then tests the combined code.
# The combined code is allowed to be ''unfinished'', but it should not be ''broken''. The combined GRNsight build should still run and show steady progress toward the fully-envisioned gene page functionality.
# Code revisions at this stage are committed and pushed to ''master''.
# When the Interaction and Integration team is satisfied with the state of the combined code, the other teams can then merge ''master'' back into their respective branches, and localized development and testing can proceed to the next phase.
# When the teams feel that they have reached another integration point, they notify the Interaction and Integration team of this and another integration iteration can take place.
# Rinse and repeat until the project is done!

[[Category:Gene hAPI]]

[[Category:Group Projects]]

Template:Gene hAPI

2017-11-30T23:34:33Z

Cwong34: Deleted QA milestones for teams other than Gene API

= Gene hAPI Helpful Links =
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

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

=Project Manager=
[ ]'''Milestone 1: Project “Scaffolding”'''

This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.

# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 12]], [[Week 14]], and [[Week 15]].
# Organize management tools for your team:
#* Workflow narratives
#* Action items
#* Testing results/reports
#** Bugs/feature requests
#** Question/answer sequences

[ ]'''Milestone 2: Periodic Updates'''

Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.

# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructors will expect you to know and be able to report on the status of each member of your team at any time.
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.
# Monitor the status of the report-in-progress and other related documentation.
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.

=Data Analyst=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[ ]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

=Quality Assurance=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[ ]'''Milestone 3: Requirements Analysis'''

As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.

* The ''entire QA guild'' should become an expert on the information that can be retrieved for a gene, so that they know how IDs should look, how certain data types will be displayed, etc. This will help them detect flaws and areas of improvement as development work proceeds.
* ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.

[ ]'''Milestone 4: On-going Testing of Respective Team Deliverables'''

The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
* ''Page Design team'': Open the prototype web page and check it for correctness and clarity. The Data Analysis guild should also be consulted to make sure that the page design and layout meets their needs when they perform their respective Data Analysis tasks.
* ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).
* For the Interaction and Integration team, prior to the first integration, QA can make sure that the “click-to-open-the-page” functionality works well and is bug-free. After the first integration, QA should work through the whole cycle of opening a gene page and examining the data that appear. QA should open multiple gene pages in the same session to make sure that successive gene page openings do not “step on” each other or leave behind obsolete data that “pollutes” future gene page loads.

=Coders=
[X]'''Milestone 0: Journal Club Presentation'''

* For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.

[ ]'''Milestone 1: Working Environment Setup'''

Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
* Node.js 8.4.0 or newer
* Code-savvy editor such as Atom or Microsoft Visual Studio Code
* Web browser with developer tools (Seaver 120 uses Google Chrome)
* '''git''' version control software
* (depends on team) '''curl''' command

Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.

[ ]'''Milestone 2: Version Control Setup'''

Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.

The Interaction and Integration team is responsible for this fork, and will do their own work on the ''master'' branch of this fork. Thus, many of the early steps in this procedure involve them, and they must accomplish these steps first before the others can proceed:

# All members of the Coder guild should acquire a GitHub account, if they don’t already have one (it’s free).
# One of the Coders of the Interaction and Integration team creates a fork of the GRNsight project.
# The Interaction and Integration team adds the GitHub accounts of all Coder guild members as ''collaborators'' on the fork.
# Once every team is a collaborator on this fork, they can then create their respective ''branches'' on the fork:
#* The Page Design team creates a branch called ''page-design''.
#* The Gene Database APIs team creates a branch called ''gene-database-apis''.
#* ''After'' the ''gene-database-apis'' branch is created, the JASPAR API team creates a branch '''from ''gene-database-apis''''' called ''jaspar-api''.

The teams will then do their work on their respective branches. The protocol for integrating your work is described in the ''Integration and Integration Testing'' milestone below.

The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.

[ ]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''

Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
# '''git clone''' the GitHub fork created in the version control setup milestone on where you plan to work on the project.
# '''cd''' into the folder that contains the cloned repository
# '''git checkout''' the branch that is assigned to you:
#* Interaction and Integration: ''master'' (no need for an explicit checkout because the clone defaults to this branch)
#* Page Design: ''page-design''
#* Gene Database APIs: ''gene-database-apis''
#* JASPAR: ''jasper-api'' (note that as instructed above, '''this should be a branch of the ''gene-database-apis'' branch''')
# Follow the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.

[ ]'''Milestone 4: Development, Implementation, and Localized Testing'''

At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:

* Page Design: ''web-client/public/html'' (this folder does not yet exist; you will need to create it) and ''web-client/test'' (in case you are able to write unit tests for your work)
** While running GRNsight, you will be able to access files in this folder through the URL http://localhost:5001/html/''filename''
* Gene Database APIs: ''web-client/public/js'' and ''web-client/test''
* JASPAR: ''web-client/public/js'' and ''web-client/test''
* Interaction and Integration: Because you are integrating the other teams’ work, you will likely interact with the entire ''web-client'' folder

For the Gene Database APIs and JASPAR teams, your work will not be visible to end-users until the first overall integration is done, so use ''unit tests'' as your initial approach for verifying that your code is working well. You will probably need to mock up your API calls so that you don’t bombard the web services with requests while unit testing. However, these sites are generally open access so you can probably write your ''initial'' set of tests using real requests and responses.

The Quality Assurance members of each team should take charge of manual testing. Specific suggested manual testing tasks are described in the [[Quality Assurance]] guild page.

The Interaction and Integration team should initially get to know the files being created and worked on by the other teams prior to the first integration milestone.

Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.

[ ]'''Milestone 5: Integration and Integration Testing'''

Integration and integration testing should take place periodically to make sure that the overall gene page project is coming together well. Most of the Coders’ work for the remainder of the semester will be a cycle of the development and integration milestones. The Interaction and Integration team is in charge of coordinating when these integrations take place. The first integration will likely be the most difficult one to perform, but it is hoped that later iterations will proceed more smoothly.

When the other teams have reached the following sub-milestones, the first integration cycle can take place. Future iterations are at the discretion of the Interaction and Integration team in coordination with how the other teams are progressing:
* Page Design: first working version of the gene page
* Gene Database APIs: first working version of the <code>getGeneInformation</code> function
* JASPAR: This team’s work does not have to participate in the first integration cycle; instead, they should integrate their work with the Gene Database APIs team whenever they have a working prototype. JASPAR functionality simply “shows up” at some future integration cycle.
* Interaction and Integration: You are not blocked from working prior to the first integration; you can work on exploring the existing GRNsight code to implement the right-click functionality that will open the gene page in a new tab or window. You can start by making this code open a blank page. Upon the first integration iteration, you can then connect that page to the gene page provided by the Page Design team.

An individual integration iteration proceeds in this way:
# The Page Design and Gene Database APIs teams issue ''pull requests'' to merge their branches with the ''master'' branch.
# The Coders guild reviews each other’s code and points out any needed revisions.
# Once all revision requests are fulfilled, the Interaction and Integration team merges the pull requests into ''master''.
# The Coders guild resolves any merge conflicts then tests the combined code.
# The combined code is allowed to be ''unfinished'', but it should not be ''broken''. The combined GRNsight build should still run and show steady progress toward the fully-envisioned gene page functionality.
# Code revisions at this stage are committed and pushed to ''master''.
# When the Interaction and Integration team is satisfied with the state of the combined code, the other teams can then merge ''master'' back into their respective branches, and localized development and testing can proceed to the next phase.
# When the teams feel that they have reached another integration point, they notify the Interaction and Integration team of this and another integration iteration can take place.
# Rinse and repeat until the project is done!

[[Category:Gene hAPI]]

[[Category:Group Projects]]

Cwong34 Week 14

2017-11-30T23:32:32Z

Cwong34: Added to electronic notebook

=Gene Database Information=
The QA's met, and we chose which information we wanted to take from which databases.

'''NCBI'''
*Locus tag
*Gene ID
*Also known as

'''UniProt'''
*Protein type/name
*Protein sequence
*Gene ID
*Similar proteins

'''Ensembl'''
*DNA sequence
*Gene description/function
*Gene ID

'''SGD'''
*Gene ID
*Gene regulation
*Gene ontology

'''JASPAR'''
*Gene ID
*Sequence logo
*Frequency matrix

=Getting Organized=
*During class, I worked on our team page to map out our deliverables and milestones. I met with our team members to check in on how they are doing and to get a better idea of where our team is in our project.
*I created the deliverables page for our team ([[Gene hAPI Deliverables]])

=Acknowledgments=

=References=
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{cwong34}}

[[Category: Journal Entry]]

Cwong34 Week 14

2017-11-30T23:25:35Z

Cwong34: Added references, acknowledgments, links, and category

=Gene Database Information=
The QA's met, and we chose which information we wanted to take from which databases.

'''NCBI'''
*Locus tag
*Gene ID

'''UniProt'''
*Protein type/name
*Protein sequence
*Gene ID
*Similar proteins

'''Ensembl'''
*DNA sequence
*Gene description
*Gene ID

'''SGD'''
*Gene ID
*Gene regulation
*Gene ontology

'''JASPAR'''
*Sequence logo
*Frequency matrix

=Acknowledgments=

=References=
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{cwong34}}

[[Category: Journal Entry]]

Template:Gene hAPI

2017-11-30T23:22:08Z

Cwong34: Created checkboxes for milestones

= Gene hAPI Helpful Links =
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

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

=Project Manager=
[ ]'''Milestone 1: Project “Scaffolding”'''

This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.

# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 12]], [[Week 14]], and [[Week 15]].
# Organize management tools for your team:
#* Workflow narratives
#* Action items
#* Testing results/reports
#** Bugs/feature requests
#** Question/answer sequences

[ ]'''Milestone 2: Periodic Updates'''

Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.

# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructors will expect you to know and be able to report on the status of each member of your team at any time.
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.
# Monitor the status of the report-in-progress and other related documentation.
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.

=Data Analyst=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[ ]'''Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight'''

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

=Quality Assurance=
[X]'''Milestone 1: Annotated Bibliography'''

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

[X]'''Milestone 2: Journal Club Presentation'''

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

[ ]'''Milestone 3: Requirements Analysis'''

As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.

* The ''entire QA guild'' should become an expert on the information that can be retrieved for a gene, so that they know how IDs should look, how certain data types will be displayed, etc. This will help them detect flaws and areas of improvement as development work proceeds.
* ''Page Design team'': QA should get to know the information that is expected to be displayed on the gene page.
* ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.
* ''JASPAR team'': QA should learn about transcription factors in general and what the JASPAR database provides in particular. They should coordinate with the Coders to learn the API initially (since this API has not been seen before in class) then work out how to retrieve relevant transcription factor information for a given gene symbol. Once the steps are learned/discovered, they should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.
* ''Interaction and integration team'': QA should be familiar with the vision of the project’s overall goal so that when they are presented with progressive builds of the project, they can test the functionality from end to end in order to detect flaws or points of improvement.

[ ]'''Milestone 4: On-going Testing of Respective Team Deliverables'''

The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
* ''Page Design team'': Open the prototype web page and check it for correctness and clarity. The Data Analysis guild should also be consulted to make sure that the page design and layout meets their needs when they perform their respective Data Analysis tasks.
* ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).
* For the Interaction and Integration team, prior to the first integration, QA can make sure that the “click-to-open-the-page” functionality works well and is bug-free. After the first integration, QA should work through the whole cycle of opening a gene page and examining the data that appear. QA should open multiple gene pages in the same session to make sure that successive gene page openings do not “step on” each other or leave behind obsolete data that “pollutes” future gene page loads.

=Coders=
[X]'''Milestone 0: Journal Club Presentation'''

* For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.

[ ]'''Milestone 1: Working Environment Setup'''

Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
* Node.js 8.4.0 or newer
* Code-savvy editor such as Atom or Microsoft Visual Studio Code
* Web browser with developer tools (Seaver 120 uses Google Chrome)
* '''git''' version control software
* (depends on team) '''curl''' command

Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.

[ ]'''Milestone 2: Version Control Setup'''

Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.

The Interaction and Integration team is responsible for this fork, and will do their own work on the ''master'' branch of this fork. Thus, many of the early steps in this procedure involve them, and they must accomplish these steps first before the others can proceed:

# All members of the Coder guild should acquire a GitHub account, if they don’t already have one (it’s free).
# One of the Coders of the Interaction and Integration team creates a fork of the GRNsight project.
# The Interaction and Integration team adds the GitHub accounts of all Coder guild members as ''collaborators'' on the fork.
# Once every team is a collaborator on this fork, they can then create their respective ''branches'' on the fork:
#* The Page Design team creates a branch called ''page-design''.
#* The Gene Database APIs team creates a branch called ''gene-database-apis''.
#* ''After'' the ''gene-database-apis'' branch is created, the JASPAR API team creates a branch '''from ''gene-database-apis''''' called ''jaspar-api''.

The teams will then do their work on their respective branches. The protocol for integrating your work is described in the ''Integration and Integration Testing'' milestone below.

The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.

[ ]'''Milestone 3: “Developer Rig” Setup and Initial As-Is Build'''

Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
# '''git clone''' the GitHub fork created in the version control setup milestone on where you plan to work on the project.
# '''cd''' into the folder that contains the cloned repository
# '''git checkout''' the branch that is assigned to you:
#* Interaction and Integration: ''master'' (no need for an explicit checkout because the clone defaults to this branch)
#* Page Design: ''page-design''
#* Gene Database APIs: ''gene-database-apis''
#* JASPAR: ''jasper-api'' (note that as instructed above, '''this should be a branch of the ''gene-database-apis'' branch''')
# Follow the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.

[ ]'''Milestone 4: Development, Implementation, and Localized Testing'''

At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:

* Page Design: ''web-client/public/html'' (this folder does not yet exist; you will need to create it) and ''web-client/test'' (in case you are able to write unit tests for your work)
** While running GRNsight, you will be able to access files in this folder through the URL http://localhost:5001/html/''filename''
* Gene Database APIs: ''web-client/public/js'' and ''web-client/test''
* JASPAR: ''web-client/public/js'' and ''web-client/test''
* Interaction and Integration: Because you are integrating the other teams’ work, you will likely interact with the entire ''web-client'' folder

For the Gene Database APIs and JASPAR teams, your work will not be visible to end-users until the first overall integration is done, so use ''unit tests'' as your initial approach for verifying that your code is working well. You will probably need to mock up your API calls so that you don’t bombard the web services with requests while unit testing. However, these sites are generally open access so you can probably write your ''initial'' set of tests using real requests and responses.

The Quality Assurance members of each team should take charge of manual testing. Specific suggested manual testing tasks are described in the [[Quality Assurance]] guild page.

The Interaction and Integration team should initially get to know the files being created and worked on by the other teams prior to the first integration milestone.

Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.

[ ]'''Milestone 5: Integration and Integration Testing'''

Integration and integration testing should take place periodically to make sure that the overall gene page project is coming together well. Most of the Coders’ work for the remainder of the semester will be a cycle of the development and integration milestones. The Interaction and Integration team is in charge of coordinating when these integrations take place. The first integration will likely be the most difficult one to perform, but it is hoped that later iterations will proceed more smoothly.

When the other teams have reached the following sub-milestones, the first integration cycle can take place. Future iterations are at the discretion of the Interaction and Integration team in coordination with how the other teams are progressing:
* Page Design: first working version of the gene page
* Gene Database APIs: first working version of the <code>getGeneInformation</code> function
* JASPAR: This team’s work does not have to participate in the first integration cycle; instead, they should integrate their work with the Gene Database APIs team whenever they have a working prototype. JASPAR functionality simply “shows up” at some future integration cycle.
* Interaction and Integration: You are not blocked from working prior to the first integration; you can work on exploring the existing GRNsight code to implement the right-click functionality that will open the gene page in a new tab or window. You can start by making this code open a blank page. Upon the first integration iteration, you can then connect that page to the gene page provided by the Page Design team.

An individual integration iteration proceeds in this way:
# The Page Design and Gene Database APIs teams issue ''pull requests'' to merge their branches with the ''master'' branch.
# The Coders guild reviews each other’s code and points out any needed revisions.
# Once all revision requests are fulfilled, the Interaction and Integration team merges the pull requests into ''master''.
# The Coders guild resolves any merge conflicts then tests the combined code.
# The combined code is allowed to be ''unfinished'', but it should not be ''broken''. The combined GRNsight build should still run and show steady progress toward the fully-envisioned gene page functionality.
# Code revisions at this stage are committed and pushed to ''master''.
# When the Interaction and Integration team is satisfied with the state of the combined code, the other teams can then merge ''master'' back into their respective branches, and localized development and testing can proceed to the next phase.
# When the teams feel that they have reached another integration point, they notify the Interaction and Integration team of this and another integration iteration can take place.
# Rinse and repeat until the project is done!

[[Category:Gene hAPI]]

[[Category:Group Projects]]

Cwong34 Week 14

2017-11-30T23:21:28Z

Cwong34: Deleted gene expression

Template:Gene hAPI

2017-11-30T23:11:23Z

Cwong34: Added deliverables page link to template

= Gene hAPI Helpful Links =
Our Deliverables: [[Gene hAPI Deliverables]]

Main Page: [[Main Page]]

Project Page: [[GRNsight Gene Page Project]]

[http://dondi.github.io/GRNsight/ GRNsight]

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

=Project Manager=
=== Milestone 1: Project “Scaffolding” ===

This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.

# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 12]], [[Week 14]], and [[Week 15]].
# Organize management tools for your team:
#* Workflow narratives
#* Action items
#* Testing results/reports
#** Bugs/feature requests
#** Question/answer sequences

=== Milestone 2: Periodic Updates ===

Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.

# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructors will expect you to know and be able to report on the status of each member of your team at any time.
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.
# Monitor the status of the report-in-progress and other related documentation.
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.

=Data Analyst=
=== Milestone 1: Annotated Bibliography ===

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

=== Milestone 2: Journal Club Presentation ===

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

=== Milestone 3: Complete Data Analysis of Dahlquist Lab Data for Visualization with GRNsight ===

* For [[Week 14]] and [[Week 15]], the Data Analysts will review and complete the microarray data analysis begun with the [[Week 8]] and [[Week 10]] assignments with the eventual goal of visualizing a gene regulatory network derived from their dataset in GRNsight. Specifically:
*# Review the ANOVA results from [[Week 8]] for accuracy, making corrections if necessary.
*# If corrections were made to the ANOVA results, re-running stem ([[Week 10]]).
*# Using the [http://www.yeastract.com YEASTRACT Database] to determine which transcription factors are candidates for regulating the genes in a cluster from stem (part of [[Week_10#Using_YEASTRACT_to_Infer_which_Transcription_Factors_Regulate_a_Cluster_of_Genes | Week 10]] that we postponed.
*# Using the [http://www.yeastract.com YEASTRACT Database] to develop a candidate gene regulatory network (part of [[Week_10#Visualizing_Your_Gene_Regulatory_Networks_with_GRNsight | Week 10]] that we postponed).
*# Using the [http://kdahlquist.github.io/GRNmap/ GRNmap] software to model the gene regulatory network (confer with Dr. Dahlquist when you are ready for this).
*# Visualizing the results with [http://dondi.github.io/GRNsight/ GRNsight].
* As the end-user of the GRNsight software, the Data Analysts will provide feedback to the QAs and Coders about the usability of the new features.

=Quality Assurance=
=== Milestone 1: Annotated Bibliography ===

* For the [[Week 11]] assignment, the Data Analysts will work with the QAs to develop an annotated bibliography of papers that perform the global transcriptional analysis of DNA microarray data in yeast.

=== Milestone 2: Journal Club Presentation ===

* For the [[Week 12]] assignment, the Data Analysts will work with the QAs to prepare a PowerPoint presentation to be delivered in class on Tuesday, November 21.

=== Milestone 3: Requirements Analysis ===

As the Coders begin their development work and the Data Analysts start working with their assigned microarray data sets, the QA team members should familiarize themselves with and help specify the expected correct functionalities of their respective teams.

* The ''entire QA guild'' should become an expert on the information that can be retrieved for a gene, so that they know how IDs should look, how certain data types will be displayed, etc. This will help them detect flaws and areas of improvement as development work proceeds.
* ''Page Design team'': QA should get to know the information that is expected to be displayed on the gene page.
* ''Gene Database APIs team'': QA should get to know how the four web service APIs are to be used in order to retrieve gene data given a gene symbol. They should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.
* ''JASPAR team'': QA should learn about transcription factors in general and what the JASPAR database provides in particular. They should coordinate with the Coders to learn the API initially (since this API has not been seen before in class) then work out how to retrieve relevant transcription factor information for a given gene symbol. Once the steps are learned/discovered, they should be able to perform these steps themselves using '''curl''' or a web browser, so that they can provide independent verification that the Coders’ work is functioning correctly.
* ''Interaction and integration team'': QA should be familiar with the vision of the project’s overall goal so that when they are presented with progressive builds of the project, they can test the functionality from end to end in order to detect flaws or points of improvement.

=== Milestone 4: On-going Testing of Respective Team Deliverables ===

The rest of the semester is expected to be an on-going process of verifying and validating the correctness of a QA member’s assigned team. Specific concerns include but are not limited to the following:
* ''Page Design team'': Open the prototype web page and check it for correctness and clarity. The Data Analysis guild should also be consulted to make sure that the page design and layout meets their needs when they perform their respective Data Analysis tasks.
* ''Gene Database APIs and JASPAR teams'': Manual testing will involve some combination of '''curl''' and web browser developer tool use in order to get to know the data returned by the various web services. The Coder members should find ways to show the Quality Assurance members the work-in-progress data returned by <code>getGeneInformation</code>, which QA can then compare to the raw web service API calls for accuracy. After the first integration milestone, QA members can examine the behavior of the prototype gene page at both the end-user and Developer Tools levels (i.e., examining network traffic to make sure the correct requests are going out with the expected responses coming in; inspecting the gene page elements to make sure that they received the correct data).
* For the Interaction and Integration team, prior to the first integration, QA can make sure that the “click-to-open-the-page” functionality works well and is bug-free. After the first integration, QA should work through the whole cycle of opening a gene page and examining the data that appear. QA should open multiple gene pages in the same session to make sure that successive gene page openings do not “step on” each other or leave behind obsolete data that “pollutes” future gene page loads.

=Coder=
=== Milestone 0: Journal Club Presentation ===

* For the [[Week 11]] assignment, the Coders (including Designers) of each team will prepare a PowerPoint presentation of their respective assigned software design/development/engineering/best practices reading to be delivered in class on Tuesday, November 14.

=== Milestone 1: Working Environment Setup ===

Coder work will require the following software. The Seaver 120 lab computers are already set up for this; this list is provided for Coders who need to work on a different computer or outside of the lab.
* Node.js 8.4.0 or newer
* Code-savvy editor such as Atom or Microsoft Visual Studio Code
* Web browser with developer tools (Seaver 120 uses Google Chrome)
* '''git''' version control software
* (depends on team) '''curl''' command

Make sure that this software is installed and operational before beginning. If any Coder needs help with any of these packages, please consult your fellow guild members or ask Dr. Dionisio.

=== Milestone 2: Version Control Setup ===

Coding work will be done on a ''fork'' of the open source [https://github.com/dondi/GRNsight GRNsight project], which is hosted on [https://github.com GitHub]. The software that interacts with GitHub to perform version control is '''git'''. If any Coder needs help with '''git''' or version control concepts in general, please consult your fellow guild members or ask Dr. Dionisio.

The Interaction and Integration team is responsible for this fork, and will do their own work on the ''master'' branch of this fork. Thus, many of the early steps in this procedure involve them, and they must accomplish these steps first before the others can proceed:

# All members of the Coder guild should acquire a GitHub account, if they don’t already have one (it’s free).
# One of the Coders of the Interaction and Integration team creates a fork of the GRNsight project.
# The Interaction and Integration team adds the GitHub accounts of all Coder guild members as ''collaborators'' on the fork.
# Once every team is a collaborator on this fork, they can then create their respective ''branches'' on the fork:
#* The Page Design team creates a branch called ''page-design''.
#* The Gene Database APIs team creates a branch called ''gene-database-apis''.
#* ''After'' the ''gene-database-apis'' branch is created, the JASPAR API team creates a branch '''from ''gene-database-apis''''' called ''jaspar-api''.

The teams will then do their work on their respective branches. The protocol for integrating your work is described in the ''Integration and Integration Testing'' milestone below.

The structure described in this milestone is a typical GitHub fork-and-branch approach which some Coders are already familiar with. If any Coder needs help with this methodology, please consult your fellow guild members or ask Dr. Dionisio.

=== Milestone 3: “Developer Rig” Setup and Initial As-Is Build ===

Before development can begin in earnest, the following initial setup steps must be performed ''per Coder'' after version control setup is complete:
# '''git clone''' the GitHub fork created in the version control setup milestone on where you plan to work on the project.
# '''cd''' into the folder that contains the cloned repository
# '''git checkout''' the branch that is assigned to you:
#* Interaction and Integration: ''master'' (no need for an explicit checkout because the clone defaults to this branch)
#* Page Design: ''page-design''
#* Gene Database APIs: ''gene-database-apis''
#* JASPAR: ''jasper-api'' (note that as instructed above, '''this should be a branch of the ''gene-database-apis'' branch''')
# Follow the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

If anyone runs into problems with this procedure, please consult with your fellow guild members or notify Dr. Dionisio.

=== Milestone 4: Development, Implementation, and Localized Testing ===

At this point, each team proceeds with their own development work. In general, each team will do most of their work (and place most of their files) in the following locations within the GRNsight repository. Some files may need to go elsewhere; check in with Dr. Dionisio if there are any file organization/location issues:

* Page Design: ''web-client/public/html'' (this folder does not yet exist; you will need to create it) and ''web-client/test'' (in case you are able to write unit tests for your work)
** While running GRNsight, you will be able to access files in this folder through the URL http://localhost:5001/html/''filename''
* Gene Database APIs: ''web-client/public/js'' and ''web-client/test''
* JASPAR: ''web-client/public/js'' and ''web-client/test''
* Interaction and Integration: Because you are integrating the other teams’ work, you will likely interact with the entire ''web-client'' folder

For the Gene Database APIs and JASPAR teams, your work will not be visible to end-users until the first overall integration is done, so use ''unit tests'' as your initial approach for verifying that your code is working well. You will probably need to mock up your API calls so that you don’t bombard the web services with requests while unit testing. However, these sites are generally open access so you can probably write your ''initial'' set of tests using real requests and responses.

The Quality Assurance members of each team should take charge of manual testing. Specific suggested manual testing tasks are described in the [[Quality Assurance]] guild page.

The Interaction and Integration team should initially get to know the files being created and worked on by the other teams prior to the first integration milestone.

Teams should perform their own internal testing (both manual and automated) on their respective files throughout development. Commit and push your work to your designated branch at appropriate intervals. Coders who are not familiar with this style of working should consult with fellow guild members or talk to Dr. Dionisio.

=== Milestone 5: Integration and Integration Testing ===

Integration and integration testing should take place periodically to make sure that the overall gene page project is coming together well. Most of the Coders’ work for the remainder of the semester will be a cycle of the development and integration milestones. The Interaction and Integration team is in charge of coordinating when these integrations take place. The first integration will likely be the most difficult one to perform, but it is hoped that later iterations will proceed more smoothly.

When the other teams have reached the following sub-milestones, the first integration cycle can take place. Future iterations are at the discretion of the Interaction and Integration team in coordination with how the other teams are progressing:
* Page Design: first working version of the gene page
* Gene Database APIs: first working version of the <code>getGeneInformation</code> function
* JASPAR: This team’s work does not have to participate in the first integration cycle; instead, they should integrate their work with the Gene Database APIs team whenever they have a working prototype. JASPAR functionality simply “shows up” at some future integration cycle.
* Interaction and Integration: You are not blocked from working prior to the first integration; you can work on exploring the existing GRNsight code to implement the right-click functionality that will open the gene page in a new tab or window. You can start by making this code open a blank page. Upon the first integration iteration, you can then connect that page to the gene page provided by the Page Design team.

An individual integration iteration proceeds in this way:
# The Page Design and Gene Database APIs teams issue ''pull requests'' to merge their branches with the ''master'' branch.
# The Coders guild reviews each other’s code and points out any needed revisions.
# Once all revision requests are fulfilled, the Interaction and Integration team merges the pull requests into ''master''.
# The Coders guild resolves any merge conflicts then tests the combined code.
# The combined code is allowed to be ''unfinished'', but it should not be ''broken''. The combined GRNsight build should still run and show steady progress toward the fully-envisioned gene page functionality.
# Code revisions at this stage are committed and pushed to ''master''.
# When the Interaction and Integration team is satisfied with the state of the combined code, the other teams can then merge ''master'' back into their respective branches, and localized development and testing can proceed to the next phase.
# When the teams feel that they have reached another integration point, they notify the Interaction and Integration team of this and another integration iteration can take place.
# Rinse and repeat until the project is done!

[[Category:Gene hAPI]]

[[Category:Group Projects]]

Gene hAPI Deliverables

2017-11-30T23:08:58Z

Cwong34: Added deliverable checklist

== Deliverables Checklist ==

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

== Our Deliverables ==
#[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
#[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

Gene hAPI Deliverables

2017-11-30T23:07:28Z

Cwong34: Added current deliverables

#[[Media:JLopezEAzingeJournalClub.pptx | The presentation - Coder/Designer]] 
#[[Media:Cold_Shock_Yeast_Genome_Response.pdf | Journal Club Week 12 Presentation - QA/Data Analyst]]

Cwong34 Week 14

2017-11-29T00:18:53Z

Cwong34: Added gene data information

Template:Cwong34

2017-11-29T00:15:11Z

Cwong34: Added week 14

Cwong34 Week 12

2017-11-21T08:05:20Z

Cwong34: Changed name of presentation link

=Article=
Sahara, T., Goda, T., & Ohgiya, S. (2002). [http://www.jbc.org/content/277/51/50015.long Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature]. Journal of Biological Chemistry, 277(51), 50015-50021.
=Presentation=
[[Media:Cold_Shock_Yeast_Genome_Response.pdf|Journal Club Presentation 2]]

=Flow Chart=
[[Image:Sahara_T_et_al_article_flowchart_CW.png]]
=Outline=
==Experiment design and procedures==
*Purchased cDNA microarray of ''Saccharomyces cervisiae'' from DNA Chip Research Inc.
*Used ''S. cervisiae''YPH500
*Grew yeast cells aerobically in YPD medium at 30 degrees celsius and shaken at 100rpm.
*YPD is made up of:
**1% yeast extract
**2% peptone
**2% glucose
*Yeast cells were grown to "mid-log phase" where they were still maturing, but not fully reproducing
*50mL of culture was taken and centrifuged to collect the cells and be used as a time 0 reference for the rest of the experiment
*The time 0 reference cells were stored at -80 degrees celsius
*The rest of culture was used for the experimental samples and was cold shocked at 10 degrees celsius
*Samples were collected at various times: 0.25, 0.5, 2, 4, and 8h
*Acidic phenol method and RNeasy Mini Kit were used to prepare the RNA
*The RNA was used to prepare fluorophore-labeled cDNA probes
*These probes marked the cells for array hybridization
*The microarrays were scanned with a laser microscope and were analyzed
*Repeated process twice
*Averaged the expression ratios of the separate experiments for final data
==Results & discussion==
*Analyzed the microarray of cDNAs of 5,803 genes in yeast genome
*There was a diauxic shift in cells that experienced cold shock
**Down-shift of some diauxic shift-inducible genes in late phase of cold shock
*Low temperature affects expression of ~25% of the yeast genes
*Number of up-regulated genes increased from 41 at 0.25h to 536 at 8h
*Number of down-regulated genes also increased from 4 at 0.25h to 488 at 8h
*Gene expression changes significantly in both ways (up & down-regulation) to adapt cells to colder environment, similar to reactions to other stresses, like heat, salinity, hydrogen peroxide, and osmotic stresses
*Table 1 shows the number of genes that significantly changed expression (2-fold or more), up-regulating or down-regulating
===Clustering analysis===
*Clustering of genes (genes that were close together) were analyzed in the ways they responded
*Genes separated into 5 different clusters (Fig. 1):
**1A: Unclassified proteins
**1B: Amino acid biosynthesis and metabolism
**1C: RNA Polymerase I & RNA processing
**1D: Ribosomal proteins
**1E: Not labeled
*Shows cooperative regulation
**1C: up-regulated in early phase (0-0.5h), then down-regulated in late phase (4-8h)
**1D & 1E: up-regulated in mid-late phase (2h & 4-8h)
===Transcription related genes===
*Looked at clusters of genes relating to RNA polymerase I & RNA processing
**All up-regulated in early phase
*Cooperative regulation of genes involved in transcription (Fig. 2)
*2 clusters of these genes:
**Down-regulating (2A, 2B, & 2D)
***2A (RNA polymerase I & RNA processing) & 2B (rRNA processing) up-regulated in early phase, then down regulated in late phase
***2D: mRNA transcription
**Up-regulating (2C)
***2C: mRNA transcription
***High up-regulating in mid phase
*Up-regulated genes that had to do with basic transcriptional functions, like genes encoding for regulatory proteins for amino acid production
*Down-regulated genes were not essential for basic life, like genes encoding heat shock transcription factor or a transcription factor for drug resistant genes
*Factors essential to transcription & processing of rRNAs were up-regulated
*Genes for synthesis and transcription regulation of mRNAs had mix responses
===Ribosomal protein related genes===
*Genes separated into four clusters (Fig. 3):
**3A & 3B: cytosolic ribosome
**3C: translational control factors
**3D: tRNA syntheatases
*3A up-regulated in early-mid phase, then down-regulated in late phase
*3B up-regulated in early-mid phase, and slightly down-regulated in the late phase
*3C continuously up-regulated starting in the early phase
*3D overall down-regulated
*Genes encoding ribosomal proteins = most of up-regulated genes at 2h
*Almost all up-regulating ribosomal proteins had similar expressions, showing cooperative regulation
*Low temperature impairs translational ability
*When genes related to ribosomal proteins and rRNA processing don't work, there is cold sensitivity
*Yeast up-regulates genes encoding ribosomal proteins, so compensates for less efficient/productive translation to overcome cold sensitivity
===Cell rescue, defense, death, and aging genes===
*Genes separated into four clusters (Fig.. 4):
**4A: not labeled
**4B & 4C: stress response - high up-regulation in mid-late phase
**4D: stress response and chaperone - high down-regulation in mid-late phase
*Heat shock protein genes (HSPs) were down-regulated in low temperatures, except HSP12 and HSP26
*This may mean HSP12 and HSP26 have different transcription regulation than other HSPs
*Graumann, et al., 1996 did similar experiment with Bacillus subtilis and found peptidyl prolyl cis/trans isomerases were induced in low temperatures, so protein folding genes were up-regulated
===Metabolism and energy production genes===
*8 clusters (Fig. 5):
**5A: nucleotide metabolism - up-regulated early-mid phase, then down-regulated
**5B & 5E: not annotated
**5C & 5D: C-compound and carbohydrate metabolism - up-regulated
**5F & 5H: amino acid metabolism - down-regulated
**5G: C-compound and carbohydrate utilization - down-regulated
*Clusters show a lot of cooperative regulation between glycogen and trehalose biosynthesis genes
**glycogen and trehalose both reserve carbohydrates
*Genes involved in glycogen production up-regulated in mid-late phases
*Curious that glycogen degradation gene (GPH1) was also up-regulated
*Tests in heat shock found even when glycogen levels were low, yeast still recylced/degraded it
*Trehalose may help protect cellular membrane, which may help to keep yeast cells intact at low temperatures
===Signal transduction genes===
*Clusters (Fig. 6):
**6A - down-regulated
**6B - little up-regulation in early phase, then down-regulation
**6C - little down-regulation in early phase, then up-regulation in late phase
*Clusters were not defined in the article
*20% of signal transduction genes changed expression significantly
*Particularly genes related to cAMP-PKA pathway were up-regulated
**increased signaling
*Increase in PKA signaling known to be response to stresses and controlled by Msn2p/4p transcription factors
*cAMP-PKA pathway involved in:
**metabolism control
**stress resistance
**cell proliferation
*Many Msn2p/4p genes up-regulated (50% of them), which had roles in:
**glycogen synthesis
**trehalose synthesis
**stress resistance
*Heat shock gene promoters are suppressed by Msn2p/4p
*Cooperative regulation in genes of Msn2p/4p and cAMP-PKA pathway that are related to stress response and biosynthesis of glycogen and trehalose
*cAMP-PKA pathway may have effect on yeast gene expression after cold shock
==Conclusion==
*Clustering analysis shows different responses in three phases:
**Early phase (0-2h) - transcription (RNA polymerase I & rRNA processing) related genes up-regulated
**Middle phase (2-4h) - ribosomal protein related genes up-regulated
**Late phase (4-8h) - stress response genes up-regulated
*This shows adaptation to environment (low temperature) involves three sequential events (the three phases)
*RNA polymerase I & rRNA processing genes respond first by up-regulating because help transcription and translation, which become less efficient when exposed to low temperature
*Ribosomal protein genes up-regulated in middle phase to further assist in maintaining translational ability
*Maintaining translation is priority to yeast in cold shock because they need to make proteins to help maintain integrity and basic functions of cells
*Stress response induced genes follow in up-regulation, so next step in yeast cells is to adapt and gain tolerance to low temperature
=Terms=
#Nucleolin: a protein associated with nucleolar in growing eukaryotic cells (NCBI, 2017).
#Hypoxia: low levels of oxygen in body tissues (Hine & Martin, 2015).
#Ubiquitin: a protein that marks which proteins are going to be broken down (Hine & Martin, 2015).
#"Mid-log" or "lag" phase: bacterial cells are maturing, but they have not yet reached their maximum reproduction rate (Hine & Martin, 2015).
#Diauxic shift: the switch of a microorganism from using one type of sugar to using another (King, et al., 2014).
#Cytosolic: contents of the fluid in the cytoplasm of a cell (King, et al., 2014).
#Peptidyl prolyl cis/trans isomerases: Enzymes that changes conformation of prolyl bonds to cis or trans, chaning the tertiary structure of a protein (Lackie, 2013).
#cAMP-PKA pathway: the activation of PKA by cAMP (Lackie, 2013).
#GTPase: enzymes that hydrolyze GTP (Lackie, 2013).
#Phosphatase: an enzyme that helps remove a phosphate group from an organic compound (Hine & Martin, 2015).
=Acknowledgments=
#I met with Dina outside of class, and we worked on our presentation together.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 17:28, 20 November 2017 (PST)

=References=
#Graumann, P., Schröder, K., Schmid, R., & Marahiel, M.A. (1996). Cold shock stress-induced proteins in Bacillus subtilis. ''Journal of Bacteriology'', 178(15), 4611-4619. doi: 10.1128/jb.178.15.4611-4619.1996
#Hine, R. & Martin, E. (Eds.). (2015). ''A Dictionary of Biology''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378
#King, R.C., Mulligan, P.K., & Stansfield, W.D. (Eds.). (2014). ''A Dictionary of Genetics''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444
#Lackie, J.L. (2013). ''The Dictionary of Cell and Molecular Biology''. In ''Science Direct''. Retrieved from http://www.sciencedirect.com/science/book/9780123849311
#LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#NCBI. (2017). Nucleolin. Retrieved November 20, 2017, from http://www.uniprot.org/uniprot/P19338
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

{{cwong34}}

[[Category: Journal Entry]]

Cwong34 Week 12

2017-11-21T08:04:03Z

Cwong34: Successfully added presentation

=Article=
Sahara, T., Goda, T., & Ohgiya, S. (2002). [http://www.jbc.org/content/277/51/50015.long Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature]. Journal of Biological Chemistry, 277(51), 50015-50021.
=Presentation=
[[Media:Cold_Shock_Yeast_Genome_Response.pdf|Journal Club Presentation]]

=Flow Chart=
[[Image:Sahara_T_et_al_article_flowchart_CW.png]]
=Outline=
==Experiment design and procedures==
*Purchased cDNA microarray of ''Saccharomyces cervisiae'' from DNA Chip Research Inc.
*Used ''S. cervisiae''YPH500
*Grew yeast cells aerobically in YPD medium at 30 degrees celsius and shaken at 100rpm.
*YPD is made up of:
**1% yeast extract
**2% peptone
**2% glucose
*Yeast cells were grown to "mid-log phase" where they were still maturing, but not fully reproducing
*50mL of culture was taken and centrifuged to collect the cells and be used as a time 0 reference for the rest of the experiment
*The time 0 reference cells were stored at -80 degrees celsius
*The rest of culture was used for the experimental samples and was cold shocked at 10 degrees celsius
*Samples were collected at various times: 0.25, 0.5, 2, 4, and 8h
*Acidic phenol method and RNeasy Mini Kit were used to prepare the RNA
*The RNA was used to prepare fluorophore-labeled cDNA probes
*These probes marked the cells for array hybridization
*The microarrays were scanned with a laser microscope and were analyzed
*Repeated process twice
*Averaged the expression ratios of the separate experiments for final data
==Results & discussion==
*Analyzed the microarray of cDNAs of 5,803 genes in yeast genome
*There was a diauxic shift in cells that experienced cold shock
**Down-shift of some diauxic shift-inducible genes in late phase of cold shock
*Low temperature affects expression of ~25% of the yeast genes
*Number of up-regulated genes increased from 41 at 0.25h to 536 at 8h
*Number of down-regulated genes also increased from 4 at 0.25h to 488 at 8h
*Gene expression changes significantly in both ways (up & down-regulation) to adapt cells to colder environment, similar to reactions to other stresses, like heat, salinity, hydrogen peroxide, and osmotic stresses
*Table 1 shows the number of genes that significantly changed expression (2-fold or more), up-regulating or down-regulating
===Clustering analysis===
*Clustering of genes (genes that were close together) were analyzed in the ways they responded
*Genes separated into 5 different clusters (Fig. 1):
**1A: Unclassified proteins
**1B: Amino acid biosynthesis and metabolism
**1C: RNA Polymerase I & RNA processing
**1D: Ribosomal proteins
**1E: Not labeled
*Shows cooperative regulation
**1C: up-regulated in early phase (0-0.5h), then down-regulated in late phase (4-8h)
**1D & 1E: up-regulated in mid-late phase (2h & 4-8h)
===Transcription related genes===
*Looked at clusters of genes relating to RNA polymerase I & RNA processing
**All up-regulated in early phase
*Cooperative regulation of genes involved in transcription (Fig. 2)
*2 clusters of these genes:
**Down-regulating (2A, 2B, & 2D)
***2A (RNA polymerase I & RNA processing) & 2B (rRNA processing) up-regulated in early phase, then down regulated in late phase
***2D: mRNA transcription
**Up-regulating (2C)
***2C: mRNA transcription
***High up-regulating in mid phase
*Up-regulated genes that had to do with basic transcriptional functions, like genes encoding for regulatory proteins for amino acid production
*Down-regulated genes were not essential for basic life, like genes encoding heat shock transcription factor or a transcription factor for drug resistant genes
*Factors essential to transcription & processing of rRNAs were up-regulated
*Genes for synthesis and transcription regulation of mRNAs had mix responses
===Ribosomal protein related genes===
*Genes separated into four clusters (Fig. 3):
**3A & 3B: cytosolic ribosome
**3C: translational control factors
**3D: tRNA syntheatases
*3A up-regulated in early-mid phase, then down-regulated in late phase
*3B up-regulated in early-mid phase, and slightly down-regulated in the late phase
*3C continuously up-regulated starting in the early phase
*3D overall down-regulated
*Genes encoding ribosomal proteins = most of up-regulated genes at 2h
*Almost all up-regulating ribosomal proteins had similar expressions, showing cooperative regulation
*Low temperature impairs translational ability
*When genes related to ribosomal proteins and rRNA processing don't work, there is cold sensitivity
*Yeast up-regulates genes encoding ribosomal proteins, so compensates for less efficient/productive translation to overcome cold sensitivity
===Cell rescue, defense, death, and aging genes===
*Genes separated into four clusters (Fig.. 4):
**4A: not labeled
**4B & 4C: stress response - high up-regulation in mid-late phase
**4D: stress response and chaperone - high down-regulation in mid-late phase
*Heat shock protein genes (HSPs) were down-regulated in low temperatures, except HSP12 and HSP26
*This may mean HSP12 and HSP26 have different transcription regulation than other HSPs
*Graumann, et al., 1996 did similar experiment with Bacillus subtilis and found peptidyl prolyl cis/trans isomerases were induced in low temperatures, so protein folding genes were up-regulated
===Metabolism and energy production genes===
*8 clusters (Fig. 5):
**5A: nucleotide metabolism - up-regulated early-mid phase, then down-regulated
**5B & 5E: not annotated
**5C & 5D: C-compound and carbohydrate metabolism - up-regulated
**5F & 5H: amino acid metabolism - down-regulated
**5G: C-compound and carbohydrate utilization - down-regulated
*Clusters show a lot of cooperative regulation between glycogen and trehalose biosynthesis genes
**glycogen and trehalose both reserve carbohydrates
*Genes involved in glycogen production up-regulated in mid-late phases
*Curious that glycogen degradation gene (GPH1) was also up-regulated
*Tests in heat shock found even when glycogen levels were low, yeast still recylced/degraded it
*Trehalose may help protect cellular membrane, which may help to keep yeast cells intact at low temperatures
===Signal transduction genes===
*Clusters (Fig. 6):
**6A - down-regulated
**6B - little up-regulation in early phase, then down-regulation
**6C - little down-regulation in early phase, then up-regulation in late phase
*Clusters were not defined in the article
*20% of signal transduction genes changed expression significantly
*Particularly genes related to cAMP-PKA pathway were up-regulated
**increased signaling
*Increase in PKA signaling known to be response to stresses and controlled by Msn2p/4p transcription factors
*cAMP-PKA pathway involved in:
**metabolism control
**stress resistance
**cell proliferation
*Many Msn2p/4p genes up-regulated (50% of them), which had roles in:
**glycogen synthesis
**trehalose synthesis
**stress resistance
*Heat shock gene promoters are suppressed by Msn2p/4p
*Cooperative regulation in genes of Msn2p/4p and cAMP-PKA pathway that are related to stress response and biosynthesis of glycogen and trehalose
*cAMP-PKA pathway may have effect on yeast gene expression after cold shock
==Conclusion==
*Clustering analysis shows different responses in three phases:
**Early phase (0-2h) - transcription (RNA polymerase I & rRNA processing) related genes up-regulated
**Middle phase (2-4h) - ribosomal protein related genes up-regulated
**Late phase (4-8h) - stress response genes up-regulated
*This shows adaptation to environment (low temperature) involves three sequential events (the three phases)
*RNA polymerase I & rRNA processing genes respond first by up-regulating because help transcription and translation, which become less efficient when exposed to low temperature
*Ribosomal protein genes up-regulated in middle phase to further assist in maintaining translational ability
*Maintaining translation is priority to yeast in cold shock because they need to make proteins to help maintain integrity and basic functions of cells
*Stress response induced genes follow in up-regulation, so next step in yeast cells is to adapt and gain tolerance to low temperature
=Terms=
#Nucleolin: a protein associated with nucleolar in growing eukaryotic cells (NCBI, 2017).
#Hypoxia: low levels of oxygen in body tissues (Hine & Martin, 2015).
#Ubiquitin: a protein that marks which proteins are going to be broken down (Hine & Martin, 2015).
#"Mid-log" or "lag" phase: bacterial cells are maturing, but they have not yet reached their maximum reproduction rate (Hine & Martin, 2015).
#Diauxic shift: the switch of a microorganism from using one type of sugar to using another (King, et al., 2014).
#Cytosolic: contents of the fluid in the cytoplasm of a cell (King, et al., 2014).
#Peptidyl prolyl cis/trans isomerases: Enzymes that changes conformation of prolyl bonds to cis or trans, chaning the tertiary structure of a protein (Lackie, 2013).
#cAMP-PKA pathway: the activation of PKA by cAMP (Lackie, 2013).
#GTPase: enzymes that hydrolyze GTP (Lackie, 2013).
#Phosphatase: an enzyme that helps remove a phosphate group from an organic compound (Hine & Martin, 2015).
=Acknowledgments=
#I met with Dina outside of class, and we worked on our presentation together.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 17:28, 20 November 2017 (PST)

=References=
#Graumann, P., Schröder, K., Schmid, R., & Marahiel, M.A. (1996). Cold shock stress-induced proteins in Bacillus subtilis. ''Journal of Bacteriology'', 178(15), 4611-4619. doi: 10.1128/jb.178.15.4611-4619.1996
#Hine, R. & Martin, E. (Eds.). (2015). ''A Dictionary of Biology''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378
#King, R.C., Mulligan, P.K., & Stansfield, W.D. (Eds.). (2014). ''A Dictionary of Genetics''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444
#Lackie, J.L. (2013). ''The Dictionary of Cell and Molecular Biology''. In ''Science Direct''. Retrieved from http://www.sciencedirect.com/science/book/9780123849311
#LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#NCBI. (2017). Nucleolin. Retrieved November 20, 2017, from http://www.uniprot.org/uniprot/P19338
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

{{cwong34}}

[[Category: Journal Entry]]

File:Cold Shock Yeast Genome Response.pdf

2017-11-21T08:03:38Z

Cwong34:

Cwong34 Week 12

2017-11-21T07:59:55Z

Cwong34:

=Article=
Sahara, T., Goda, T., & Ohgiya, S. (2002). [http://www.jbc.org/content/277/51/50015.long Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature]. Journal of Biological Chemistry, 277(51), 50015-50021.
=Presentation=
[[Media:Cold_shock_Yeast_Genome_Response.ppt|Journal Club Presentation]]
=Flow Chart=
[[Image:Sahara_T_et_al_article_flowchart_CW.png]]
=Outline=
==Experiment design and procedures==
*Purchased cDNA microarray of ''Saccharomyces cervisiae'' from DNA Chip Research Inc.
*Used ''S. cervisiae''YPH500
*Grew yeast cells aerobically in YPD medium at 30 degrees celsius and shaken at 100rpm.
*YPD is made up of:
**1% yeast extract
**2% peptone
**2% glucose
*Yeast cells were grown to "mid-log phase" where they were still maturing, but not fully reproducing
*50mL of culture was taken and centrifuged to collect the cells and be used as a time 0 reference for the rest of the experiment
*The time 0 reference cells were stored at -80 degrees celsius
*The rest of culture was used for the experimental samples and was cold shocked at 10 degrees celsius
*Samples were collected at various times: 0.25, 0.5, 2, 4, and 8h
*Acidic phenol method and RNeasy Mini Kit were used to prepare the RNA
*The RNA was used to prepare fluorophore-labeled cDNA probes
*These probes marked the cells for array hybridization
*The microarrays were scanned with a laser microscope and were analyzed
*Repeated process twice
*Averaged the expression ratios of the separate experiments for final data
==Results & discussion==
*Analyzed the microarray of cDNAs of 5,803 genes in yeast genome
*There was a diauxic shift in cells that experienced cold shock
**Down-shift of some diauxic shift-inducible genes in late phase of cold shock
*Low temperature affects expression of ~25% of the yeast genes
*Number of up-regulated genes increased from 41 at 0.25h to 536 at 8h
*Number of down-regulated genes also increased from 4 at 0.25h to 488 at 8h
*Gene expression changes significantly in both ways (up & down-regulation) to adapt cells to colder environment, similar to reactions to other stresses, like heat, salinity, hydrogen peroxide, and osmotic stresses
*Table 1 shows the number of genes that significantly changed expression (2-fold or more), up-regulating or down-regulating
===Clustering analysis===
*Clustering of genes (genes that were close together) were analyzed in the ways they responded
*Genes separated into 5 different clusters (Fig. 1):
**1A: Unclassified proteins
**1B: Amino acid biosynthesis and metabolism
**1C: RNA Polymerase I & RNA processing
**1D: Ribosomal proteins
**1E: Not labeled
*Shows cooperative regulation
**1C: up-regulated in early phase (0-0.5h), then down-regulated in late phase (4-8h)
**1D & 1E: up-regulated in mid-late phase (2h & 4-8h)
===Transcription related genes===
*Looked at clusters of genes relating to RNA polymerase I & RNA processing
**All up-regulated in early phase
*Cooperative regulation of genes involved in transcription (Fig. 2)
*2 clusters of these genes:
**Down-regulating (2A, 2B, & 2D)
***2A (RNA polymerase I & RNA processing) & 2B (rRNA processing) up-regulated in early phase, then down regulated in late phase
***2D: mRNA transcription
**Up-regulating (2C)
***2C: mRNA transcription
***High up-regulating in mid phase
*Up-regulated genes that had to do with basic transcriptional functions, like genes encoding for regulatory proteins for amino acid production
*Down-regulated genes were not essential for basic life, like genes encoding heat shock transcription factor or a transcription factor for drug resistant genes
*Factors essential to transcription & processing of rRNAs were up-regulated
*Genes for synthesis and transcription regulation of mRNAs had mix responses
===Ribosomal protein related genes===
*Genes separated into four clusters (Fig. 3):
**3A & 3B: cytosolic ribosome
**3C: translational control factors
**3D: tRNA syntheatases
*3A up-regulated in early-mid phase, then down-regulated in late phase
*3B up-regulated in early-mid phase, and slightly down-regulated in the late phase
*3C continuously up-regulated starting in the early phase
*3D overall down-regulated
*Genes encoding ribosomal proteins = most of up-regulated genes at 2h
*Almost all up-regulating ribosomal proteins had similar expressions, showing cooperative regulation
*Low temperature impairs translational ability
*When genes related to ribosomal proteins and rRNA processing don't work, there is cold sensitivity
*Yeast up-regulates genes encoding ribosomal proteins, so compensates for less efficient/productive translation to overcome cold sensitivity
===Cell rescue, defense, death, and aging genes===
*Genes separated into four clusters (Fig.. 4):
**4A: not labeled
**4B & 4C: stress response - high up-regulation in mid-late phase
**4D: stress response and chaperone - high down-regulation in mid-late phase
*Heat shock protein genes (HSPs) were down-regulated in low temperatures, except HSP12 and HSP26
*This may mean HSP12 and HSP26 have different transcription regulation than other HSPs
*Graumann, et al., 1996 did similar experiment with Bacillus subtilis and found peptidyl prolyl cis/trans isomerases were induced in low temperatures, so protein folding genes were up-regulated
===Metabolism and energy production genes===
*8 clusters (Fig. 5):
**5A: nucleotide metabolism - up-regulated early-mid phase, then down-regulated
**5B & 5E: not annotated
**5C & 5D: C-compound and carbohydrate metabolism - up-regulated
**5F & 5H: amino acid metabolism - down-regulated
**5G: C-compound and carbohydrate utilization - down-regulated
*Clusters show a lot of cooperative regulation between glycogen and trehalose biosynthesis genes
**glycogen and trehalose both reserve carbohydrates
*Genes involved in glycogen production up-regulated in mid-late phases
*Curious that glycogen degradation gene (GPH1) was also up-regulated
*Tests in heat shock found even when glycogen levels were low, yeast still recylced/degraded it
*Trehalose may help protect cellular membrane, which may help to keep yeast cells intact at low temperatures
===Signal transduction genes===
*Clusters (Fig. 6):
**6A - down-regulated
**6B - little up-regulation in early phase, then down-regulation
**6C - little down-regulation in early phase, then up-regulation in late phase
*Clusters were not defined in the article
*20% of signal transduction genes changed expression significantly
*Particularly genes related to cAMP-PKA pathway were up-regulated
**increased signaling
*Increase in PKA signaling known to be response to stresses and controlled by Msn2p/4p transcription factors
*cAMP-PKA pathway involved in:
**metabolism control
**stress resistance
**cell proliferation
*Many Msn2p/4p genes up-regulated (50% of them), which had roles in:
**glycogen synthesis
**trehalose synthesis
**stress resistance
*Heat shock gene promoters are suppressed by Msn2p/4p
*Cooperative regulation in genes of Msn2p/4p and cAMP-PKA pathway that are related to stress response and biosynthesis of glycogen and trehalose
*cAMP-PKA pathway may have effect on yeast gene expression after cold shock
==Conclusion==
*Clustering analysis shows different responses in three phases:
**Early phase (0-2h) - transcription (RNA polymerase I & rRNA processing) related genes up-regulated
**Middle phase (2-4h) - ribosomal protein related genes up-regulated
**Late phase (4-8h) - stress response genes up-regulated
*This shows adaptation to environment (low temperature) involves three sequential events (the three phases)
*RNA polymerase I & rRNA processing genes respond first by up-regulating because help transcription and translation, which become less efficient when exposed to low temperature
*Ribosomal protein genes up-regulated in middle phase to further assist in maintaining translational ability
*Maintaining translation is priority to yeast in cold shock because they need to make proteins to help maintain integrity and basic functions of cells
*Stress response induced genes follow in up-regulation, so next step in yeast cells is to adapt and gain tolerance to low temperature
=Terms=
#Nucleolin: a protein associated with nucleolar in growing eukaryotic cells (NCBI, 2017).
#Hypoxia: low levels of oxygen in body tissues (Hine & Martin, 2015).
#Ubiquitin: a protein that marks which proteins are going to be broken down (Hine & Martin, 2015).
#"Mid-log" or "lag" phase: bacterial cells are maturing, but they have not yet reached their maximum reproduction rate (Hine & Martin, 2015).
#Diauxic shift: the switch of a microorganism from using one type of sugar to using another (King, et al., 2014).
#Cytosolic: contents of the fluid in the cytoplasm of a cell (King, et al., 2014).
#Peptidyl prolyl cis/trans isomerases: Enzymes that changes conformation of prolyl bonds to cis or trans, chaning the tertiary structure of a protein (Lackie, 2013).
#cAMP-PKA pathway: the activation of PKA by cAMP (Lackie, 2013).
#GTPase: enzymes that hydrolyze GTP (Lackie, 2013).
#Phosphatase: an enzyme that helps remove a phosphate group from an organic compound (Hine & Martin, 2015).
=Acknowledgments=
#I met with Dina outside of class, and we worked on our presentation together.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 17:28, 20 November 2017 (PST)

=References=
#Graumann, P., Schröder, K., Schmid, R., & Marahiel, M.A. (1996). Cold shock stress-induced proteins in Bacillus subtilis. ''Journal of Bacteriology'', 178(15), 4611-4619. doi: 10.1128/jb.178.15.4611-4619.1996
#Hine, R. & Martin, E. (Eds.). (2015). ''A Dictionary of Biology''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378
#King, R.C., Mulligan, P.K., & Stansfield, W.D. (Eds.). (2014). ''A Dictionary of Genetics''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444
#Lackie, J.L. (2013). ''The Dictionary of Cell and Molecular Biology''. In ''Science Direct''. Retrieved from http://www.sciencedirect.com/science/book/9780123849311
#LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#NCBI. (2017). Nucleolin. Retrieved November 20, 2017, from http://www.uniprot.org/uniprot/P19338
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

{{cwong34}}

[[Category: Journal Entry]]

Cwong34 Week 12

2017-11-21T07:51:07Z

Cwong34: Added presentation section

=Article=
Sahara, T., Goda, T., & Ohgiya, S. (2002). [http://www.jbc.org/content/277/51/50015.long Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature]. Journal of Biological Chemistry, 277(51), 50015-50021.
=Presentation=

=Flow Chart=
[[Image:Sahara_T_et_al_article_flowchart_CW.png]]
=Outline=
==Experiment design and procedures==
*Purchased cDNA microarray of ''Saccharomyces cervisiae'' from DNA Chip Research Inc.
*Used ''S. cervisiae''YPH500
*Grew yeast cells aerobically in YPD medium at 30 degrees celsius and shaken at 100rpm.
*YPD is made up of:
**1% yeast extract
**2% peptone
**2% glucose
*Yeast cells were grown to "mid-log phase" where they were still maturing, but not fully reproducing
*50mL of culture was taken and centrifuged to collect the cells and be used as a time 0 reference for the rest of the experiment
*The time 0 reference cells were stored at -80 degrees celsius
*The rest of culture was used for the experimental samples and was cold shocked at 10 degrees celsius
*Samples were collected at various times: 0.25, 0.5, 2, 4, and 8h
*Acidic phenol method and RNeasy Mini Kit were used to prepare the RNA
*The RNA was used to prepare fluorophore-labeled cDNA probes
*These probes marked the cells for array hybridization
*The microarrays were scanned with a laser microscope and were analyzed
*Repeated process twice
*Averaged the expression ratios of the separate experiments for final data
==Results & discussion==
*Analyzed the microarray of cDNAs of 5,803 genes in yeast genome
*There was a diauxic shift in cells that experienced cold shock
**Down-shift of some diauxic shift-inducible genes in late phase of cold shock
*Low temperature affects expression of ~25% of the yeast genes
*Number of up-regulated genes increased from 41 at 0.25h to 536 at 8h
*Number of down-regulated genes also increased from 4 at 0.25h to 488 at 8h
*Gene expression changes significantly in both ways (up & down-regulation) to adapt cells to colder environment, similar to reactions to other stresses, like heat, salinity, hydrogen peroxide, and osmotic stresses
*Table 1 shows the number of genes that significantly changed expression (2-fold or more), up-regulating or down-regulating
===Clustering analysis===
*Clustering of genes (genes that were close together) were analyzed in the ways they responded
*Genes separated into 5 different clusters (Fig. 1):
**1A: Unclassified proteins
**1B: Amino acid biosynthesis and metabolism
**1C: RNA Polymerase I & RNA processing
**1D: Ribosomal proteins
**1E: Not labeled
*Shows cooperative regulation
**1C: up-regulated in early phase (0-0.5h), then down-regulated in late phase (4-8h)
**1D & 1E: up-regulated in mid-late phase (2h & 4-8h)
===Transcription related genes===
*Looked at clusters of genes relating to RNA polymerase I & RNA processing
**All up-regulated in early phase
*Cooperative regulation of genes involved in transcription (Fig. 2)
*2 clusters of these genes:
**Down-regulating (2A, 2B, & 2D)
***2A (RNA polymerase I & RNA processing) & 2B (rRNA processing) up-regulated in early phase, then down regulated in late phase
***2D: mRNA transcription
**Up-regulating (2C)
***2C: mRNA transcription
***High up-regulating in mid phase
*Up-regulated genes that had to do with basic transcriptional functions, like genes encoding for regulatory proteins for amino acid production
*Down-regulated genes were not essential for basic life, like genes encoding heat shock transcription factor or a transcription factor for drug resistant genes
*Factors essential to transcription & processing of rRNAs were up-regulated
*Genes for synthesis and transcription regulation of mRNAs had mix responses
===Ribosomal protein related genes===
*Genes separated into four clusters (Fig. 3):
**3A & 3B: cytosolic ribosome
**3C: translational control factors
**3D: tRNA syntheatases
*3A up-regulated in early-mid phase, then down-regulated in late phase
*3B up-regulated in early-mid phase, and slightly down-regulated in the late phase
*3C continuously up-regulated starting in the early phase
*3D overall down-regulated
*Genes encoding ribosomal proteins = most of up-regulated genes at 2h
*Almost all up-regulating ribosomal proteins had similar expressions, showing cooperative regulation
*Low temperature impairs translational ability
*When genes related to ribosomal proteins and rRNA processing don't work, there is cold sensitivity
*Yeast up-regulates genes encoding ribosomal proteins, so compensates for less efficient/productive translation to overcome cold sensitivity
===Cell rescue, defense, death, and aging genes===
*Genes separated into four clusters (Fig.. 4):
**4A: not labeled
**4B & 4C: stress response - high up-regulation in mid-late phase
**4D: stress response and chaperone - high down-regulation in mid-late phase
*Heat shock protein genes (HSPs) were down-regulated in low temperatures, except HSP12 and HSP26
*This may mean HSP12 and HSP26 have different transcription regulation than other HSPs
*Graumann, et al., 1996 did similar experiment with Bacillus subtilis and found peptidyl prolyl cis/trans isomerases were induced in low temperatures, so protein folding genes were up-regulated
===Metabolism and energy production genes===
*8 clusters (Fig. 5):
**5A: nucleotide metabolism - up-regulated early-mid phase, then down-regulated
**5B & 5E: not annotated
**5C & 5D: C-compound and carbohydrate metabolism - up-regulated
**5F & 5H: amino acid metabolism - down-regulated
**5G: C-compound and carbohydrate utilization - down-regulated
*Clusters show a lot of cooperative regulation between glycogen and trehalose biosynthesis genes
**glycogen and trehalose both reserve carbohydrates
*Genes involved in glycogen production up-regulated in mid-late phases
*Curious that glycogen degradation gene (GPH1) was also up-regulated
*Tests in heat shock found even when glycogen levels were low, yeast still recylced/degraded it
*Trehalose may help protect cellular membrane, which may help to keep yeast cells intact at low temperatures
===Signal transduction genes===
*Clusters (Fig. 6):
**6A - down-regulated
**6B - little up-regulation in early phase, then down-regulation
**6C - little down-regulation in early phase, then up-regulation in late phase
*Clusters were not defined in the article
*20% of signal transduction genes changed expression significantly
*Particularly genes related to cAMP-PKA pathway were up-regulated
**increased signaling
*Increase in PKA signaling known to be response to stresses and controlled by Msn2p/4p transcription factors
*cAMP-PKA pathway involved in:
**metabolism control
**stress resistance
**cell proliferation
*Many Msn2p/4p genes up-regulated (50% of them), which had roles in:
**glycogen synthesis
**trehalose synthesis
**stress resistance
*Heat shock gene promoters are suppressed by Msn2p/4p
*Cooperative regulation in genes of Msn2p/4p and cAMP-PKA pathway that are related to stress response and biosynthesis of glycogen and trehalose
*cAMP-PKA pathway may have effect on yeast gene expression after cold shock
==Conclusion==
*Clustering analysis shows different responses in three phases:
**Early phase (0-2h) - transcription (RNA polymerase I & rRNA processing) related genes up-regulated
**Middle phase (2-4h) - ribosomal protein related genes up-regulated
**Late phase (4-8h) - stress response genes up-regulated
*This shows adaptation to environment (low temperature) involves three sequential events (the three phases)
*RNA polymerase I & rRNA processing genes respond first by up-regulating because help transcription and translation, which become less efficient when exposed to low temperature
*Ribosomal protein genes up-regulated in middle phase to further assist in maintaining translational ability
*Maintaining translation is priority to yeast in cold shock because they need to make proteins to help maintain integrity and basic functions of cells
*Stress response induced genes follow in up-regulation, so next step in yeast cells is to adapt and gain tolerance to low temperature
=Terms=
#Nucleolin: a protein associated with nucleolar in growing eukaryotic cells (NCBI, 2017).
#Hypoxia: low levels of oxygen in body tissues (Hine & Martin, 2015).
#Ubiquitin: a protein that marks which proteins are going to be broken down (Hine & Martin, 2015).
#"Mid-log" or "lag" phase: bacterial cells are maturing, but they have not yet reached their maximum reproduction rate (Hine & Martin, 2015).
#Diauxic shift: the switch of a microorganism from using one type of sugar to using another (King, et al., 2014).
#Cytosolic: contents of the fluid in the cytoplasm of a cell (King, et al., 2014).
#Peptidyl prolyl cis/trans isomerases: Enzymes that changes conformation of prolyl bonds to cis or trans, chaning the tertiary structure of a protein (Lackie, 2013).
#cAMP-PKA pathway: the activation of PKA by cAMP (Lackie, 2013).
#GTPase: enzymes that hydrolyze GTP (Lackie, 2013).
#Phosphatase: an enzyme that helps remove a phosphate group from an organic compound (Hine & Martin, 2015).
=Acknowledgments=
#I met with Dina outside of class, and we worked on our presentation together.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Cwong34|Cwong34]] ([[User talk:Cwong34|talk]]) 17:28, 20 November 2017 (PST)

=References=
#Graumann, P., Schröder, K., Schmid, R., & Marahiel, M.A. (1996). Cold shock stress-induced proteins in Bacillus subtilis. ''Journal of Bacteriology'', 178(15), 4611-4619. doi: 10.1128/jb.178.15.4611-4619.1996
#Hine, R. & Martin, E. (Eds.). (2015). ''A Dictionary of Biology''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780198714378.001.0001/acref-9780198714378
#King, R.C., Mulligan, P.K., & Stansfield, W.D. (Eds.). (2014). ''A Dictionary of Genetics''. In ''Oxford Reference''. Retrieved from http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444
#Lackie, J.L. (2013). ''The Dictionary of Cell and Molecular Biology''. In ''Science Direct''. Retrieved from http://www.sciencedirect.com/science/book/9780123849311
#LMU BioDB 2017. (2017). Week 12. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
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Gene hAPI

2017-11-21T07:27:18Z

Cwong34: Removed extra files section

Gene hAPI

2017-11-21T07:26:36Z

Cwong34: Added signature

Gene hAPI

2017-11-21T07:25:53Z

Cwong34: Added week 12 summary and files section