LMU BioDB 2017 - User contributions [en]

JASPAR the Friendly Ghost Final Deliverables

2017-12-15T23:48:05Z

Qlanners: added wiki signature

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_Week_15|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
[[Media:Api.txt|JASPAR team's code (as well as hAPI's code)]] | December 15, 2017 
==README that summarizes the functionality of your team's new feature==
[[Media:README.txt|Readme.txt]] | December 15, 2017 
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST) 
*[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:48, 15 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

QLanners Week 15

2017-12-15T23:45:00Z

Qlanners: added link for statement page

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
==Electronic Notebook==
On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#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''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#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.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used [https://www.lucidchart.com Lucid Chart] to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, our group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my [[QLanners_individual_statement|statement of work page]] and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minute corrections). 

Fields unable to retrieve. (This list is incomplete, as I tried to connect with Eddie and John through text on multiple occasions, but never got any responses):
*Similar Proteins (UniProt)

==Acknowledgements==
*All of the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team members for the collaborative effort.
*[[User:Cazinge|Eddie A]] and [[User:Johnllopez616|John Lopez]] for providing me information on what (if any) fields were unretrievable from certain databases.
*[[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dondi]] for their help and guidance throughout the semester.
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 11:11, 14 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 
Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com 

==Links==
{{Template:QLannersLinks}}

QLanners Week 15

2017-12-15T23:43:28Z

Qlanners: typos

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
==Electronic Notebook==
On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#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''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#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.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used [https://www.lucidchart.com Lucid Chart] to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, our group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my statement of work page and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minute corrections). 

Fields unable to retrieve. (This list is incomplete, as I tried to connect with Eddie and John through text on multiple occasions, but never got any responses):
*Similar Proteins (UniProt)

==Acknowledgements==
*All of the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team members for the collaborative effort.
*[[User:Cazinge|Eddie A]] and [[User:Johnllopez616|John Lopez]] for providing me information on what (if any) fields were unretrievable from certain databases.
*[[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dondi]] for their help and guidance throughout the semester.
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 11:11, 14 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 
Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com 

==Links==
{{Template:QLannersLinks}}

JASPAR the Friendly Ghost

2017-12-15T23:40:35Z

Qlanners: added a new source for week 15

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]]) 
[[Media:README.txt|Readme.txt]] | December 15, 2017 
[[Media:Api.txt|Our code for this feature (also hAPI team's code)]] | December 15, 2017 

==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====
The beginning of this week was spent finishing our feature. We ran into some issues, but we worked it out with King Dondi. Once we were done with the feature, we spent some time making sure that the other teams knew what to expect from JASPAR specifically, so that they could properly put it on the final page product. After we were done with this part of the assignment, we then began to work on the power point presentation. We all worked together at first and then split off to work on our specific parts. We presented, and still didn't celebrate because we had to write an essay. The essay was a lot of repetition and formalities.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:13, 15 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:09, 15 December 2017 (PST)

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
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#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
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===Week 12===
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#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
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#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
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#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
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#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
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#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

QLanners individual statement

2017-12-15T23:39:20Z

Qlanners: added bold

=Statement of Work=
Filling both the roles of a [[Project_Manager|project manager]] and [[Quality_Assurance|quality assurance]] member for the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team, I contributed in a number of ways to the success of our team. The initial contribution I added to our team was in the form of the literature review on the effects of cold shock on yeast, which I conducted alongside our teams [Data_Analysis|data analyst], [[User:Aporras1|Antonio Porras]]. The first step of this process was an in-depth literature search which was conducted with the use of three credible online resources ([https://scholar.google.com Google Scholar], [https://www.ncbi.nlm.nih.gov/pubmed/ Pubmed], and [https://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=7ACK4DWEcZEwu7n1d3m&preferencesSaved= Web of Science]). The results of these searches can be seen in my [[QLanners_Week_11|week 11]] electronic notebook. After having found a number of articles on the topic, we honed in on one article in particular, namely [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/ 'Genome-Wide Analysis of the Yeast Transcriptome Upon Heat and Cold Shock'], and created and presented a journal club presentation to the class. [Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|This presentation]], and our work which went into creating this presentation, can be viewed on my [[QLanners_Week_12|week 12]] electronic lab notebook.

After the journal club presentation had been completed, I primarily functioned as the coordinator for all of the team milestones and deadlines. To better facilitate this task, I met with each member of my team and came up with a number of checkpoints. These checkpoints were then formatted into a calendar which can be seen on the [[JASPAR_the_Friendly_Ghost|team page]]. In addition to this initial planning, I also performed a secondary planning for the final group deliverables, as I outlined what I forecasted as being each team members primary responsibilities in my [[QLanners_Week_15|week 15]] electronic notebook. Along with these more explicitly visible examples of managing, I also spearheaded the efforts of collaboration outside of class, working to text in our team group chat to coordinate best times to meet and ensure that each individual member of the team was performing their assignments.

While coordinating the team's efforts was a primary role, I also served in a number of other areas. Another major task that I completed was to identify the fields we wished to retrieve from each of the five databases ([http://jaspar.genereg.net JASPAR], [https://www.ncbi.nlm.nih.gov NCBI], [https://www.ensembl.org Ensembl], [http://www.uniprot.org UniProt], and [https://www.yeastgenome.org SGD]) we would be utilizing. I worked closely with the other project managers ([[User:Emmatyrnauer|Emma Tyrnauer]], [[User:Kwrigh35|Katie Wright]], and [[User:Hhinsch|Hayden Hinsch]]) to visit each of the five databases and determine which database was best suited for which information. I outlined all of the fields we identified for each database on my [[QLanners_Week_14|week 14]] electronic journal page. after having compiled an initial list, I ran these fields past [[User:Kdahlquist|Dr. Dahlquist]] to determine if there were any other fields which she wished to be included. And after having added all of these fields that Dr. Dahlquist requested, I shared this information with both our JASPAR API team and the [[Gene_hAPI|Gene hAPI]] team so that they could develop the appropriate code. Along with just providing a list for each of the desired fields, I also included the answer to each field for a sample gene 'hsf1', which was done to assist the coders in recognizing which parts of each database to pull. Furthermore, I also followed up with the coders continuously (namely my two team members, [[User:Cazinge|Eddie A]], and [[User:Johnllopez616|John]]) to help them with any issues they had and ensure that their code was working. I also noted which fields they were unable to retrieve for any reason, and documented these fields in my [[QLanners_Week_15|week 15]] electronic notebook so that they could be identified as potential fields to retrieve in the future.

In regards to the final project, I created and kept our [[JASPAR_the_Friendly_Ghost_Final_Deliverables|team deliverable page]], along with working on a number of parts of the final deliverables. Specifically, I created google docs/slides for both the final paper and ppt, and invited my team members to each of them. In the ppt, I worked on crafting the entire introduction section along with the conclusion and outline (which the help of my team members of course). Along with focusing primarily on my portion of the ppt, I also assisted my team members in their parts, providing feedback and checking for format/grammar issues. The [[Media:JASPAR The Friendly Ghost Group Presentation.pdf|final group presentation]] can be found on our team page. For the paper, I focused on primarily the same sections that I did for the ppt, writing the introduction and the bulk of the conclusion. I also wrote my own methods portion.

Overall, as both project manager and quality assurance member, I played a number of roles on the team.

[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:52, 14 December 2017 (PST)
=Assessment of Project=
*What worked and what didn't work?
**As a team there were a number of things that worked, but also a couple things that did not work so well. Focusing first on the positive stuff, we worked very well as a team and communicated well. All team members were willing and able to meet on multiple occasions, which made for very good work sessions and allowed for us as a team to stay on task. Furthermore, everyone in the team was very willing to take on their responsibilities. Additionally, all team members were very respectful of each other, providing constructive criticism on presentation slides, areas of the paper, or other areas of our work. These forms of constructive criticism allowed for our deliverables to be improved without creating any tension between the team members. However, while overall we worked very well, there were a few difficulties we ran into. The first difficulty was with our coders, who initially had troubles with the execution of their code. They had to work with Dr. Dondi to overcome this difficulty, and although it eventually worked in the end, it cut into the time that they were able t help on the group presentation and paper in class and thus put a bit more stress on the project manager and data analyst. Furthermore, there was definitely some difficulty communicating the importance of the two aspects of the project to all of the team members. What I mean by this is that the data analyst had little idea what the coders were doing and vice versa. While our collaborative work on the presentation definitely helped clear this issue up a bit, there was never full understanding for all teammates on the purpose and methods of the two facets of the project.
*What would you do differently if you could do it all over again?
**If I could do it all over again, I would definitely begin the project by establishing what the purpose of our research was with all of the team members. In this way, we all would have known exactly what we are striving for as a team and would have better been able to understand how the two parts of the project were going to fit together. This would have made the creating of our final presentation and paper much easier, as I wouldn't have had to spend so much time explaining the connection to my teammates. And although there was more general understanding towards the end, the project still felt very separated throughout the whole process. Another idea would have been to have small group meetings between our group at the beginning or end of each class to update each person in the team on your status so that we were always on track. This also would have helped me as project manager to ensure everyone was on pace with their deadlines.
*Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
**Content: What is the quality of the work?
***I felt that we as a team delivered very high qualities of work, especially given the time constraints on this project (and the fact that we all had to coordinate our work around a very busy time of year). Our coders successfully retrieved all of the desired fields from JASPAR that I as quality assurance identified. In that sense, we completed our goal as a team in regards to the GRNsight feature. In regards to the group presentation and paper, I felt we did a very good job al circumstances considered. It was incredibly difficult to coordinate the work for these projects, as everyone was very busy with finals, but we still managed to meet as a team on multiple occasions. Furthermore, I felt that we as a team paid very good attention to the details, not only handing in all the deliverables but also ensuring that the deliverables met all of the requirements.
**Organization: Comment on the organization of the project and of your group's wiki pages.
***While at the beginning of the project our wiki page was definitely lacking a bit, after I was given some time to work on the page, I felt our team page became very easy to navigate and held all of the necessary information in a very logical manner. Additionally, all of us completed every weekly journal and were sure to link all of these to our team page, further enhancing our level of organization. If there were any deficits in the organization, it probably came in regards to our work on the final paper. As everyone was busy towards the end of the week, our organization was a bit tough to maintain at times, however, I feel we did a good job of finishing strong and ensuring to clean everything up before finalizing it.
**Completeness: Did your team achieve all of the project objectives? Why or why not?
***Yes we completed all deliverables. There was a bit of a time crunch at the end, but thanks to good communication and teamwork we managed to get everything turned in on time.

[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:52, 14 December 2017 (PST)

=Reflection of the Process=
*What did you learn?
**With your head (biological or computer science principles)
***There was a variety of information that I learned a lot more about in this course. Speaking first to the biological portion of the course, while I have taken a number of biology and chemistry classes before, I have not taken a genetics course before. So this course was a bit of a crash course on how genetics works. Being that I am very interested in data analysis, I was particularly interested in all of the data that is collected in genomics, and the unique ways that this data is analyzed. While I loved learning about the background and different techniques that go into genomics (such as microarrays, STEM, etc.), I would like to gain a deeper understanding of exactly what each of the statistical steps we took in the class did. I felt at times like I was just blindly following a list of steps and would have appreciated a deeper sense of understanding.In regards to the computer science principles, I learned a decent amount about how API calls work, and how you can use navigation features to easily work through the code of a website. I also enjoyed getting a short little intro the basics of how HTML works.
**With your heart (personal qualities and teamwork qualities that make things work or not work)?
***Having a number of partner and group projects throughout the semester, I learned a lot about the importance of starting things early. Especially early on in the class, there were several occasions were I was cramming to get things done on the night before things were due. Furthermore, as project manager of my team, I gained invaluable experience about the importance of ensuring constant communication between team members. I found that the more we stayed in touch the more productive we were as a team. These are skills that I will certainly take with me into whatever I end up pursuing as a career.
**With your hands (technical skills)?
***While I did practice a few technical skills in this class, in all honesty, this is the part of the course I was a bit disappointed in. I was hoping to have much more exposure to writing code and doing data analysis. While there was a decent amount of code writing, since I was not a coder for the final project, I felt like I really did not gain any meaningful technical skills in regards to programming. However, I did at least gain knowledge about how to use developer tools to easily navigate a website which I'm sure will come in handy down the road. And in regards to the data analysis, while there was a week with quite a bit of Excel work, as I explained earlier, the Excel worked felt like I was just mindlessly following a script. This kind of technical skills will not stick with me, as I honestly was not sure what the meaning behind each manipulation was.
*What lesson will you take away from this project that you will still use a year from now?
**Overall, it is not the technical skills but rather the experience I gained as a team member and project manager that I will be using a year from now. I definitely learned a lot about the importance of planning ahead, setting milestones, and identifying deadlines. Furthermore, I learned a lot about the importance of constant communication to ensure that these deadlines are met and that the work is done right. While I do wish that I would have gained a bit more technical skills from the class, I cannot take for granted the amount that these managerial skills will aid me going forward.

[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:52, 14 December 2017 (PST)

=Acknowledgements=
*The members of the JASPAR the Friendly Ghost team for all their hard work.
*The template on the GRNsight Gene Page Project Deliverables for the format of this page. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:38, 15 December 2017 (PST)

=Resources=
LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

=Links=
{{Template:QLannersLinks}}

QLanners individual statement

2017-12-15T23:38:31Z

Qlanners: added two sections

=Statement of Work=
Filling both the roles of a [[Project_Manager|project manager]] and [[Quality_Assurance|quality assurance]] member for the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team, I contributed in a number of ways to the success of our team. The initial contribution I added to our team was in the form of the literature review on the effects of cold shock on yeast, which I conducted alongside our teams [Data_Analysis|data analyst], [[User:Aporras1|Antonio Porras]]. The first step of this process was an in-depth literature search which was conducted with the use of three credible online resources ([https://scholar.google.com Google Scholar], [https://www.ncbi.nlm.nih.gov/pubmed/ Pubmed], and [https://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=7ACK4DWEcZEwu7n1d3m&preferencesSaved= Web of Science]). The results of these searches can be seen in my [[QLanners_Week_11|week 11]] electronic notebook. After having found a number of articles on the topic, we honed in on one article in particular, namely [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/ 'Genome-Wide Analysis of the Yeast Transcriptome Upon Heat and Cold Shock'], and created and presented a journal club presentation to the class. [Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|This presentation]], and our work which went into creating this presentation, can be viewed on my [[QLanners_Week_12|week 12]] electronic lab notebook.

After the journal club presentation had been completed, I primarily functioned as the coordinator for all of the team milestones and deadlines. To better facilitate this task, I met with each member of my team and came up with a number of checkpoints. These checkpoints were then formatted into a calendar which can be seen on the [[JASPAR_the_Friendly_Ghost|team page]]. In addition to this initial planning, I also performed a secondary planning for the final group deliverables, as I outlined what I forecasted as being each team members primary responsibilities in my [[QLanners_Week_15|week 15]] electronic notebook. Along with these more explicitly visible examples of managing, I also spearheaded the efforts of collaboration outside of class, working to text in our team group chat to coordinate best times to meet and ensure that each individual member of the team was performing their assignments.

While coordinating the team's efforts was a primary role, I also served in a number of other areas. Another major task that I completed was to identify the fields we wished to retrieve from each of the five databases ([http://jaspar.genereg.net JASPAR], [https://www.ncbi.nlm.nih.gov NCBI], [https://www.ensembl.org Ensembl], [http://www.uniprot.org UniProt], and [https://www.yeastgenome.org SGD]) we would be utilizing. I worked closely with the other project managers ([[User:Emmatyrnauer|Emma Tyrnauer]], [[User:Kwrigh35|Katie Wright]], and [[User:Hhinsch|Hayden Hinsch]]) to visit each of the five databases and determine which database was best suited for which information. I outlined all of the fields we identified for each database on my [[QLanners_Week_14|week 14]] electronic journal page. after having compiled an initial list, I ran these fields past [[User:Kdahlquist|Dr. Dahlquist]] to determine if there were any other fields which she wished to be included. And after having added all of these fields that Dr. Dahlquist requested, I shared this information with both our JASPAR API team and the [[Gene_hAPI|Gene hAPI]] team so that they could develop the appropriate code. Along with just providing a list for each of the desired fields, I also included the answer to each field for a sample gene 'hsf1', which was done to assist the coders in recognizing which parts of each database to pull. Furthermore, I also followed up with the coders continuously (namely my two team members, [[User:Cazinge|Eddie A]], and [[User:Johnllopez616|John]]) to help them with any issues they had and ensure that their code was working. I also noted which fields they were unable to retrieve for any reason, and documented these fields in my [[QLanners_Week_15|week 15]] electronic notebook so that they could be identified as potential fields to retrieve in the future.

In regards to the final project, I created and kept our [[JASPAR_the_Friendly_Ghost_Final_Deliverables|team deliverable page]], along with working on a number of parts of the final deliverables. Specifically, I created google docs/slides for both the final paper and ppt, and invited my team members to each of them. In the ppt, I worked on crafting the entire introduction section along with the conclusion and outline (which the help of my team members of course). Along with focusing primarily on my portion of the ppt, I also assisted my team members in their parts, providing feedback and checking for format/grammar issues. The [[Media:JASPAR The Friendly Ghost Group Presentation.pdf|final group presentation]] can be found on our team page. For the paper, I focused on primarily the same sections that I did for the ppt, writing the introduction and the bulk of the conclusion. I also wrote my own methods portion.

Overall, as both project manager and quality assurance member, I played a number of roles on the team.

[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:52, 14 December 2017 (PST)
=Assessment of Project=
*What worked and what didn't work?
**As a team there were a number of things that worked, but also a couple things that did not work so well. Focusing first on the positive stuff, we worked very well as a team and communicated well. All team members were willing and able to meet on multiple occasions, which made for very good work sessions and allowed for us as a team to stay on task. Furthermore, everyone in the team was very willing to take on their responsibilities. Additionally, all team members were very respectful of each other, providing constructive criticism on presentation slides, areas of the paper, or other areas of our work. These forms of constructive criticism allowed for our deliverables to be improved without creating any tension between the team members. However, while overall we worked very well, there were a few difficulties we ran into. The first difficulty was with our coders, who initially had troubles with the execution of their code. They had to work with Dr. Dondi to overcome this difficulty, and although it eventually worked in the end, it cut into the time that they were able t help on the group presentation and paper in class and thus put a bit more stress on the project manager and data analyst. Furthermore, there was definitely some difficulty communicating the importance of the two aspects of the project to all of the team members. What I mean by this is that the data analyst had little idea what the coders were doing and vice versa. While our collaborative work on the presentation definitely helped clear this issue up a bit, there was never full understanding for all teammates on the purpose and methods of the two facets of the project.
*What would you do differently if you could do it all over again?
**If I could do it all over again, I would definitely begin the project by establishing what the purpose of our research was with all of the team members. In this way, we all would have known exactly what we are striving for as a team and would have better been able to understand how the two parts of the project were going to fit together. This would have made the creating of our final presentation and paper much easier, as I wouldn't have had to spend so much time explaining the connection to my teammates. And although there was more general understanding towards the end, the project still felt very separated throughout the whole process. Another idea would have been to have small group meetings between our group at the beginning or end of each class to update each person in the team on your status so that we were always on track. This also would have helped me as project manager to ensure everyone was on pace with their deadlines.
*Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
**Content: What is the quality of the work?
***I felt that we as a team delivered very high qualities of work, especially given the time constraints on this project (and the fact that we all had to coordinate our work around a very busy time of year). Our coders successfully retrieved all of the desired fields from JASPAR that I as quality assurance identified. In that sense, we completed our goal as a team in regards to the GRNsight feature. In regards to the group presentation and paper, I felt we did a very good job al circumstances considered. It was incredibly difficult to coordinate the work for these projects, as everyone was very busy with finals, but we still managed to meet as a team on multiple occasions. Furthermore, I felt that we as a team paid very good attention to the details, not only handing in all the deliverables but also ensuring that the deliverables met all of the requirements.
**Organization: Comment on the organization of the project and of your group's wiki pages.
***While at the beginning of the project our wiki page was definitely lacking a bit, after I was given some time to work on the page, I felt our team page became very easy to navigate and held all of the necessary information in a very logical manner. Additionally, all of us completed every weekly journal and were sure to link all of these to our team page, further enhancing our level of organization. If there were any deficits in the organization, it probably came in regards to our work on the final paper. As everyone was busy towards the end of the week, our organization was a bit tough to maintain at times, however, I feel we did a good job of finishing strong and ensuring to clean everything up before finalizing it.
**Completeness: Did your team achieve all of the project objectives? Why or why not?
***Yes we completed all deliverables. There was a bit of a time crunch at the end, but thanks to good communication and teamwork we managed to get everything turned in on time.

[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:52, 14 December 2017 (PST)

=Reflection of the Process=
*What did you learn?
**With your head (biological or computer science principles)
***There was a variety of information that I learned a lot more about in this course. Speaking first to the biological portion of the course, while I have taken a number of biology and chemistry classes before, I have not taken a genetics course before. So this course was a bit of a crash course on how genetics works. Being that I am very interested in data analysis, I was particularly interested in all of the data that is collected in genomics, and the unique ways that this data is analyzed. While I loved learning about the background and different techniques that go into genomics (such as microarrays, STEM, etc.), I would like to gain a deeper understanding of exactly what each of the statistical steps we took in the class did. I felt at times like I was just blindly following a list of steps and would have appreciated a deeper sense of understanding.In regards to the computer science principles, I learned a decent amount about how API calls work, and how you can use navigation features to easily work through the code of a website. I also enjoyed getting a short little intro the basics of how HTML works.
**With your heart (personal qualities and teamwork qualities that make things work or not work)?
***Having a number of partner and group projects throughout the semester, I learned a lot about the importance of starting things early. Especially early on in the class, there were several occasions were I was cramming to get things done on the night before things were due. Furthermore, as project manager of my team, I gained invaluable experience about the importance of ensuring constant communication between team members. I found that the more we stayed in touch the more productive we were as a team. These are skills that I will certainly take with me into whatever I end up pursuing as a career.
**With your hands (technical skills)?
***While I did practice a few technical skills in this class, in all honesty, this is the part of the course I was a bit disappointed in. I was hoping to have much more exposure to writing code and doing data analysis. While there was a decent amount of code writing, since I was not a coder for the final project, I felt like I really did not gain any meaningful technical skills in regards to programming. However, I did at least gain knowledge about how to use developer tools to easily navigate a website which I'm sure will come in handy down the road. And in regards to the data analysis, while there was a week with quite a bit of Excel work, as I explained earlier, the Excel worked felt like I was just mindlessly following a script. This kind of technical skills will not stick with me, as I honestly was not sure what the meaning behind each manipulation was.
*What lesson will you take away from this project that you will still use a year from now?
**Overall, it is not the technical skills but rather the experience I gained as a team member and project manager that I will be using a year from now. I definitely learned a lot about the importance of planning ahead, setting milestones, and identifying deadlines. Furthermore, I learned a lot about the importance of constant communication to ensure that these deadlines are met and that the work is done right. While I do wish that I would have gained a bit more technical skills from the class, I cannot take for granted the amount that these managerial skills will aid me going forward.

[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:52, 14 December 2017 (PST)

=Acknowledgements=
*The members of the JASPAR the Friendly Ghost team for all their hard work.
*The template on the GRNsight Gene Page Project Deliverables for the format of this page. 
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:38, 15 December 2017 (PST)

=Resources=
LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

=Links=
{{Template:QLannersLinks}}

QLanners Week 15

2017-12-15T05:16:03Z

Qlanners: added short snippet to end of journal

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
==Electronic Notebook==
On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#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''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#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.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used [https://www.lucidchart.com Lucid Chart] to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, out group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my statement of work page, and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minure corrections). 

Fields unable to retreive. (This list is incomplete, as I tried to connect with Eddie and John through text on multiple occasions, but never got any responses):
*Similar Proteins (UniProt)

==Acknowledgements==
*All of the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team members for the collaborative effort.
*[[User:Cazinge|Eddie A]] and [[User:Johnllopez616|John Lopez]] for providing me information on what (if any) fields were unretrievable from certain databases.
*[[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dondi]] for their help and guidance throughout the semester.
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 11:11, 14 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 
Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com 

==Links==
{{Template:QLannersLinks}}

JASPAR the Friendly Ghost

2017-12-15T05:14:59Z

Qlanners: added link to qlanners week 15

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
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#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
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#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
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#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
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#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T05:13:21Z

Qlanners: added reflection and exec summary week 15 for quinn

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

QLanners individual statement

2017-12-15T04:52:22Z

Qlanners: added last section and wiki signature to each section

QLanners individual statement

2017-12-14T19:48:25Z

Qlanners: added links

QLanners individual statement

2017-12-14T19:32:53Z

Qlanners: did my reflection of the process

QLanners Week 15

2017-12-14T19:11:10Z

Qlanners: added acknowledgements and references and links

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
==Electronic Notebook==
On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#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''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#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.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used [https://www.lucidchart.com Lucid Chart] to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, out group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my statement of work page, and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minure corrections). 

Fields unable to retreive:
*Similar Proteins (UniProt)

==Acknowledgements==
*All of the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team members for the collaborative effort.
*[[User:Cazinge|Eddie A]] and [[User:Johnllopez616|John Lopez]] for providing me information on what (if any) fields were unretrievable from certain databases.
*[[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dondi]] for their help and guidance throughout the semester.
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 11:11, 14 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 
Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com 

==Links==
{{Template:QLannersLinks}}

QLanners Week 15

2017-12-14T19:04:54Z

Qlanners: Added more dialogue to the electronic notebook

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
==Electronic Notebook==
On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#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''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#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.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used [https://www.lucidchart.com Lucid Chart] to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, out group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my statement of work page, and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minure corrections).
Fields unable to retreive:
*Similar Proteins (UniProt)

File:JASPAR The Friendly Ghost Group Presentation.pdf

2017-12-12T21:44:54Z

Qlanners: Qlanners uploaded a new version of File:JASPAR The Friendly Ghost Group Presentation.pdf

Final Group Presentation For JASPAR the Friendly Ghost team

File:JASPAR The Friendly Ghost Group Presentation.pdf

2017-12-12T21:41:57Z

Qlanners: Qlanners uploaded a new version of File:JASPAR The Friendly Ghost Group Presentation.pdf

Final Group Presentation For JASPAR the Friendly Ghost team

QLanners individual statement

2017-12-12T16:49:25Z

Qlanners: fixed typo

QLanners individual statement

2017-12-12T07:56:12Z

Qlanners: small missing parentheses

QLanners individual statement

2017-12-12T07:54:29Z

Qlanners: added my statement of work

JASPAR the Friendly Ghost Final Deliverables

2017-12-12T07:19:49Z

Qlanners: made another typo edit

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1 individual statement|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]
==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
==README that summarizes the functionality of your team's new feature==
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost Final Deliverables

2017-12-12T07:19:28Z

Qlanners: made a typo edit

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1 individual statement|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]
==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
==README that summarizes the functionality of your team's new feature==
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to these the microarray results files==

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Ebachour Week 15

2017-12-12T07:16:06Z

Qlanners: added link for final group presentation

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017

Simonwro120 Week 15

2017-12-12T07:14:40Z

Qlanners: added link for final group presentation

=Electronic Notebook=
==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
==Tuesday==

==Thursday==

== Acknowledgements ==
*I worked with my homework partner, Eddie Bachoura, on this assignment.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*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). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

QLanners Week 15

2017-12-12T07:12:49Z

Qlanners: added link for group presentation

JASPAR the Friendly Ghost Final Deliverables

2017-12-12T07:11:19Z

Qlanners: added link for the final presentation

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1 individual statement|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]
==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
==README that summarizes the functionality of your team's new feature==
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebook corresponding to these the microarray results files==

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-12T07:09:28Z

Qlanners: added date for final presentation link

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-12T07:08:49Z

Qlanners: added link for final group presentation

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]]
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

File:JASPAR The Friendly Ghost Group Presentation.pdf

2017-12-12T07:07:26Z

Qlanners: Final Group Presentation For JASPAR the Friendly Ghost team

Final Group Presentation For JASPAR the Friendly Ghost team

QLanners Week 15

2017-12-09T22:13:44Z

Qlanners: added fields unable to retrieve section

On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#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''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#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.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

Fields unable to retreive:
*Similar Proteins (UniProt)

QLanners Week 15

2017-12-08T00:17:15Z

Qlanners: adding spacing

QLanners Week 15

2017-12-08T00:16:09Z

Qlanners: added a summary for thursday december 7th

On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#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''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#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.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report:
[[File:Biological databases paper outline.jpg | 300px]]

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

GRNsight Gene Page Project Deliverables

2017-12-07T23:59:12Z

Qlanners: fixed spacing

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

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

=== Grading ===

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

== Group Report ==

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

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

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

=== Style Sheet ===

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

=== Cover Page ===

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

=== Abstract ===

Provide an abstract of no more than 500 words.

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be 3-5 pages long (double-spaced). The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

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

* States importance of the problem
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page as the answer to this problem.
* States the question the paper is trying to address
** In this case you want to discover new information about the microarray data using GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.

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

=== Results ===

This section will summarize the results of the project. This section will include figures, tables, and a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.

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

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

==== Coding Results ====

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

=== Discussion ===

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

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

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

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 12 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructors using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What are the best points about the presentation's organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Individual Assessment and Reflection ==

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

=== Statement of Work ===

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

=== Assessment of Project ===

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

=== Reflection on the Process ===

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

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

GRNsight Gene Page Project Deliverables

2017-12-07T23:58:44Z

Qlanners: added signature to uploaded outline image

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

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

=== Grading ===

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

== Group Report ==

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

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

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

=== Style Sheet ===

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

=== Cover Page ===

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

=== Abstract ===

Provide an abstract of no more than 500 words.

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be 3-5 pages long (double-spaced). The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

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

* States importance of the problem
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page as the answer to this problem.
* States the question the paper is trying to address
** In this case you want to discover new information about the microarray data using GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.

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

=== Results ===

This section will summarize the results of the project. This section will include figures, tables, and a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.

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

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

==== Coding Results ====

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

=== Discussion ===

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

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

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

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 12 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructors using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What are the best points about the presentation's organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Individual Assessment and Reflection ==

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

=== Statement of Work ===

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

=== Assessment of Project ===

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

=== Reflection on the Process ===

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

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

GRNsight Gene Page Project Deliverables

2017-12-07T23:58:05Z

Qlanners: added image of updated outline for group report

{{GRNsight Gene Page Project Links}}

== Deliverables Checklist ==

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

=== Grading ===

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

== Group Report ==

Image of updated outline for Group Report
[[File:Biological databases paper outline.jpg | 500px]]

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

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

=== Style Sheet ===

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

=== Cover Page ===

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

=== Abstract ===

Provide an abstract of no more than 500 words.

=== Introduction ===

The introduction gives the background information necessary to understand your report and should be 3-5 pages long (double-spaced). The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

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

* States importance of the problem
* States what is known about the problem
** Give an overview of what is known about the regulation of the transcriptional response to cold shock in yeast from the Data Analyst/QA's [[Week 12]] journal club article and the information presented by Dr. Dahlquist in class.
** Discuss how you will approach this by analyzing yeast cold shock microarray data from the Dahlquist Lab.
* States what is unknown about the problem
** Which transcription factors belong in the gene regulatory network that controls the cold shock response in yeast is still unknown.
* States clues that suggest how to approach the unknown
** Introduce GRNsight and the GRNsight gene page as the answer to this problem.
* States the question the paper is trying to address
** In this case you want to discover new information about the microarray data using GRNsight.
* State the approach
** Give an overview of your team's contribution to GRNsight and why it is needed.

=== Materials & Methods ===

This section will summarize the entire workflow for the project. This needs to be a '''''narrative description''''' of what your team actually did, but not a step-by-step protocol. We are following the standards of reproducible research such that someone else with the appropriate expertise could reproduce what you did given the information in your Materials and Methods section. You can consider your audience to be the fellow members of your class.

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

=== Results ===

This section will summarize the results of the project. This section will include figures, tables, and a '''''narrative description''''' of the results shown in those figures and tables. You should:
* Number each of the figures sequentially and number each of the tables sequentially in order from first mention in the text. You can either embed your figures and tables in the appropriate place in the text or put them all at the end. Do not mix both styles, however.
* Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.

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

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

==== Coding Results ====

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

=== Discussion ===

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

=== Conclusions ===

* Write a concluding paragraph that summarizes the overall project and your findings.
* What future directions would you take if you were to continue this project?

=== Acknowledgments ===

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

=== References ===

* This section lists all of the references cited in the text of the report (and only those references cited in the paper). Follow the [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] handout for general principles.
* Remember that you need to cite anything for which you are not the original source. Generally, in the introduction, you should aim for a minimum of two in-text citations per paragraph. You may reference the course web site using the appropriate format for a web reference.
* List your references in alphabetical order by first author using the APA style that you have been using throughout the semester. Note that the proper format must be followed for both articles and websites, just URLs are not sufficient.

== PowerPoint Presentation ==

Each team of students will prepare and give a 20 minute PowerPoint presentation to report the results of their project on Tuesday, December 12 at 2:00-4:00 PM.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation) and include the following content:
** Title slide that gives the main take-home message as the title of your presentation, the authors, date, and venue (course number and title).
** Outline slide that is a summary of take-home messages of your talk (should mirror your conclusion slide)
** The body of your talk (organized in a logical flow, not necessarily in the order given below).
*** Introduce the importance/significance of the problem and give background on cold shock in yeast. You can draw from the DA/QA's journal club presentation. This should follow the logic of the Introduction section of your group paper.
*** Show a combined flow chart of the tasks/milestones completed by your group (see Materials and Methods of group paper).
*** Show the table of ANOVA results.
*** Show the screenshot of the overall clustering results and the cluster you focused on .
*** Show a table of the GO results from that cluster, giving an interpretation.
*** Show the table of regulatory transcription factors in your network and their p values for enrichment.
*** Show the unweighted and weighted networks in GRNsight (with the genes arranged in the same way in each figure)
*** Explain the new feature for GRNsight created by your team with code snippets and screenshots as appropriate.
** Conclusion slide that mirrors your outline
** Future directions
** Acknowledgments
** References
* '''''Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am, Tuesday, December 12.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructors using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What are the best points about the presentation's organization, visuals, and delivery? Please give at least 2 specific examples.
*# What points need improvement? Please give at least 2 specific examples.
* We expect that you will take the feedback from your previous presentation into account when doing this presentation.

== Individual Assessment and Reflection ==

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

=== Statement of Work ===

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

=== Assessment of Project ===

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

=== Reflection on the Process ===

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

{{GRNsight Gene Page Project Links}}

[[Category:Group Projects]]

File:Biological databases paper outline.jpg

2017-12-07T23:52:01Z

Qlanners: outline of what to include in updated biological databases paper

outline of what to include in updated biological databases paper

JASPAR the Friendly Ghost Final Deliverables

2017-12-05T23:20:55Z

Qlanners: created individual statement pages for each team member and added team and class links

Template:JASPAR the Friendly Ghost Links

2017-12-05T23:20:33Z

Qlanners: added the final deliverables page to team template

JASPAR the Friendly Ghost Final Deliverables

2017-12-05T23:16:10Z

Qlanners: Created section headers for deliverables

==Group Report (.doc, .docx or .pdf file)==
==Individual statements of work, assessments, reflections==
==Group PowerPoint presentation==
==Code==
==README that summarizes the functionality of your team's new feature==
==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==
==GRNmap output workbook==
==Electronic notebook corresponding to these the microarray results files==

JASPAR the Friendly Ghost

2017-12-05T23:13:33Z

Qlanners: created a final project deliverables page

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
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===Week 12===
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#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

QLanners Week 15

2017-12-05T23:09:01Z

Qlanners: created an outline for who will work on each deliverable

Template:QLannersLinks

2017-12-05T22:56:59Z

Qlanners: added week 15 links

Template:JASPAR the Friendly Ghost Links

2017-12-05T22:55:58Z

Qlanners: made week 15 pages for everyone

QLanners Week 14

2017-12-05T07:00:07Z

Qlanners: edited a acknowledgements

==Electronic Journal==
In order to determine what fields should be taken from each database, I worked closely with [[User:Cwong34|Corinne Wong]] and [[User:Kwrigh35|Katie Wright]]. We the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database. All of the fields are included in the below section as a bullet. Each bullet is followed by a portion of italicized text which corresponds to the information of that field for HSF1.

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

===Fields to Pull From Each Database===
We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*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]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''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''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*Gene Map 
[[File:Saccharomycescerevisiae HSF1.pdf]]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions 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 Enhancement: 1''
***''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)''

===Other Tasks===
Along with working on determining what to include in each page, I corresponded this information with our coders. I also worked on adding milestones to the calendar on our team page. In order to add these milestones, I reviewed all of the deliverables that we have to produce and then collaborated with my teammates to determine an effective and realistic timeline for accomplishing these goals.

==Acknowledgements==
#I checked base with [[User:Aporras1|Antonio]] each day in class to ensure that he was on track and knew what his objectives were. I also collaborated with Antonio to update his tasks on the team calendar to better reflect the path he was on. 
#I checked base with my teammates [[User:Simonwro120|Simon]] and [[User:Ebachour|Eddie]] in class both days to track their progress and ensure that the team calender accurately reflected their progress. I also checked base again with Eddie outside of class on Monday December 4, to ensure that they were making good progress and to see what they needed help/guidance with.
#[[User:Kdahlquist|Dr. Dahlquist]] for her guidnance regarding what information should be pulled from each website.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:56, 4 December 2017 (PST)

==References==
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Links==
{{Template:QLannersLinks}}

QLanners Week 14

2017-12-05T06:55:09Z

Qlanners: edited a file

==Electronic Journal==
In order to determine what fields should be taken from each database, I worked closely with [[User:Cwong34|Corinne Wong]] and [[User:Kwrigh35|Katie Wright]]. We the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database. All of the fields are included in the below section as a bullet. Each bullet is followed by a portion of italicized text which corresponds to the information of that field for HSF1.

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

===Fields to Pull From Each Database===
We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*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]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''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''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*Gene Map 
[[File:Saccharomycescerevisiae HSF1.pdf]]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions 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 Enhancement: 1''
***''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)''

===Other Tasks===
Along with working on determining what to include in each page, I corresponded this information with our coders. I also worked on adding milestones to the calendar on our team page. In order to add these milestones, I reviewed all of the deliverables that we have to produce and then collaborated with my teammates to determine an effective and realistic timeline for accomplishing these goals.

==Acknowledgements==
#I checked base with [[User:Aporras1|Antonio]] each day in class to ensure that he was on track and knew what his objectives were. I also collaborated with Antonio to update his tasks on the team calendar to better reflect the path he was on. 
#I checked base with my teammates [[User:Simonwro120|Simon]] and [[User:Ebachour|Eddie]] in class both days to track their progress and ensure that the team calender accurately reflected their progress. I also checked base again with Simon outside of class on Monday December 4, to ensure that they were making good progress and to see what they needed help/guidance with.
#[[User:Kdahlquist|Dr. Dahlquist]] for her guidnance regarding what information should be pulled from each website.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:56, 4 December 2017 (PST)

==References==
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Links==
{{Template:QLannersLinks}}

JASPAR the Friendly Ghost

2017-12-05T06:50:27Z

Qlanners: added numbers for week 14 sources

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
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#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-05T05:06:33Z

Qlanners: added sources for week 14

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, we both me and Eddie B. know where the API guidelines are for for JASPAR and what content we need to produce.

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-05T05:05:02Z

Qlanners: added exec summary and reflection portions for qlanners

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, we both me and Eddie B. know where the API guidelines are for for JASPAR and what content we need to produce.

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#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.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, 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
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
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#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
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==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

QLanners Week 14

2017-12-05T04:56:15Z

Qlanners: added acknowledgements and other tasks section and links

==Electronic Journal==
In order to determine what fields should be taken from each database, I worked closely with [[User:Cwong34|Corinne Wong]] and [[User:Kwrigh35|Katie Wright]]. We the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database. All of the fields are included in the below section as a bullet. Each bullet is followed by a portion of italicized text which corresponds to the information of that field for HSF1.

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

===Fields to Pull From Each Database===
We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*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]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''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''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*'Gene Map 
[File:Saccharomycescerevisiae HSF1.pdf]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions 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 Enhancement: 1''
***''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)''

===Other Tasks===
Along with working on determining what to include in each page, I corresponded this information with our coders. I also worked on adding milestones to the calendar on our team page. In order to add these milestones, I reviewed all of the deliverables that we have to produce and then collaborated with my teammates to determine an effective and realistic timeline for accomplishing these goals.

==Acknowledgements==
#I checked base with [[User:Aporras1|Antonio]] each day in class to ensure that he was on track and knew what his objectives were. I also collaborated with Antonio to update his tasks on the team calendar to better reflect the path he was on. 
#I checked base with my teammates [[User:Simonwro120|Simon]] and [[User:Ebachour|Eddie]] in class both days to track their progress and ensure that the team calender accurately reflected their progress. I also checked base again with Simon outside of class on Monday December 4, to ensure that they were making good progress and to see what they needed help/guidance with.
#[[User:Kdahlquist|Dr. Dahlquist]] for her guidnance regarding what information should be pulled from each website.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 20:56, 4 December 2017 (PST)

==References==
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Links==
{{Template:QLannersLinks}}

QLanners Week 14

2017-12-05T04:45:08Z

Qlanners: added references an titles of other sections

==Electronic Journal==
In order to determine what fields should be taken from each database, I worked closely with [[User:Cwong34|Corinne Wong]] and [[User:Kwrigh35|Katie Wright]]. We the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database. All of the fields are included in the below section as a bullet. Each bullet is followed by a portion of italicized text which corresponds to the information of that field for HSF1.

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

===Fields to Pull From Each Database===
We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*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]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''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''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*'Gene Map 
[File:Saccharomycescerevisiae HSF1.pdf]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions 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 Enhancement: 1''
***''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)''

===Other Tasks===
Along with working on determining what

==Acknowledgements==

==References==
Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

QLanners Week 14

2017-12-05T04:09:18Z

Qlanners: added rest of answers for hsf1 gene

Used the gene HSF1, which is a transcription factor, to determine which fields should be pulled from each database. All of the fields are followed by a portion of italicized text which corresponds to the information of that field for HSF1.

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

We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*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]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''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''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*'Gene Map 
[File:Saccharomycescerevisiae HSF1.pdf]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions 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 Enhancement: 1''
***''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)''