LMU BioDB 2017 - User contributions [en]

File:LCI Group Report.pdf

2017-12-15T20:52:46Z

Bhamilton18: Bhamilton18 uploaded a new version of File:LCI Group Report.pdf

up to date group report name and current draft

Lights, Camera, InterACTION! Deliverables

2017-12-15T07:52:09Z

Bhamilton18: added note about individual statement

===Group Report and Presentation===
Group Report: [[Media:LCI_Group_Report.pdf]]

Presentation: [[Media:LCI Presentation.pdf]]

===Individual Statements===
[[Emma's Individual Statement]]

Blair's Individual Statement: '''emailed'''

===Code and README===
[https://github.com/bhamilton18/GRNsight GRNsight GitHub Fork]

[https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/gene/integrationREADME.md README.md File]

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Final regulation matrix: [[Media:Final_regulationmatrix_trimmed.xlsx]]
# Input workbook: [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]
# Output workbook after Matlab: [[Media:Matlab_output_17-genes_39-edges_teamINT_Sigmoid_estimation_output_copy.xlsx]]
# Weighted and unweighted GRNmap images: [[Media:GRNmap_images_emma_t.zip]]
# Individual gene .jpg's from matlab output: [[Media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

File:LCI Group Report.pdf

2017-12-15T07:11:39Z

Bhamilton18: up to date group report name and current draft

up to date group report name and current draft

Lights, Camera, InterACTION! Deliverables

2017-12-15T07:10:47Z

Bhamilton18: updated group report name

===Group Report and Presentation===
Group Report: [[Media:LCI_Group_Report.pdf]]

Presentation: [[Media:LCI Presentation.pdf]]

===Individual Statements===
[[Emma's Individual Statement]]

===Code and README===
[https://github.com/bhamilton18/GRNsight GRNsight GitHub Fork]

[https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/gene/integrationREADME.md README.md File]

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Final regulation matrix: [[Media:Final_regulationmatrix_trimmed.xlsx]]
# Input workbook: [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]
# Output workbook after Matlab: [[Media:Matlab_output_17-genes_39-edges_teamINT_Sigmoid_estimation_output_copy.xlsx]]
# Weighted and unweighted GRNmap images: [[Media:GRNmap_images_emma_t.zip]]
# Individual gene .jpg's from matlab output: [[Media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

Lights, Camera, InterACTION! Deliverables

2017-12-15T07:08:12Z

Bhamilton18: added draft of group report

===Group Report and Presentation===
Group Report: [[Media:Group_Report.pdf]]

Presentation: [[Media:LCI Presentation.pdf]]

===Individual Statements===
[[Emma's Individual Statement]]

===Code and README===
[https://github.com/bhamilton18/GRNsight GRNsight GitHub Fork]

[https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/gene/integrationREADME.md README.md File]

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Final regulation matrix: [[Media:Final_regulationmatrix_trimmed.xlsx]]
# Input workbook: [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]
# Output workbook after Matlab: [[Media:Matlab_output_17-genes_39-edges_teamINT_Sigmoid_estimation_output_copy.xlsx]]
# Weighted and unweighted GRNmap images: [[Media:GRNmap_images_emma_t.zip]]
# Individual gene .jpg's from matlab output: [[Media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

File:Group Report.pdf

2017-12-15T07:06:57Z

Bhamilton18: Current group report, still draft mode

Current group report, still draft mode

Lights, Camera, InterACTION! Deliverables

2017-12-15T07:00:44Z

Bhamilton18: Added github code and read link

===Group Report and Presentation===
Presentation: [[Media:LCI Presentation.pdf]]

===Individual Statements===
[[Emma's Individual Statement]]

===Code and README===
[https://github.com/bhamilton18/GRNsight GRNsight GitHub Fork]

[https://github.com/bhamilton18/GRNsight/blob/master/web-client/public/gene/integrationREADME.md README.md File]

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Final regulation matrix: [[Media:Final_regulationmatrix_trimmed.xlsx]]
# Input workbook: [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]
# Output workbook after Matlab: [[Media:Matlab_output_17-genes_39-edges_teamINT_Sigmoid_estimation_output_copy.xlsx]]
# Weighted and unweighted GRNmap images: [[Media:GRNmap_images_emma_t.zip]]
# Individual gene .jpg's from matlab output: [[Media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

Bhamilton18 Week 12

2017-12-14T06:06:57Z

Bhamilton18: Added signature to acknowledgments

==Electronic Notebook==
For this week's assignment [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked on the [[Coder]] Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project.

===Milestone 0===
#This portion of the assignment was completed in the [[Week 11]] journal club presentation. The powerpoint can be found here:
#*[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]

===Milestone 1===
#This portion required our individual computers had the correct software to complete the project.
#The following were already on my computer/downloaded to meet the requirements of this milestone:
#* Node.js 8.4.0
#* Code-savvy editor (Atom for my case)
#* Web browser with developer tools (Chrome for my case)
#* '''git''' version control software
#* '''curl''' command

===Milestone 2===
#This portion required me to '''fork''' the open source [https://github.com/dondi/GRNsight GRNsight project].
#*This is found in the top right corner of the GRNsight GitHub project page.
#I added each coder as a collaborator on the project to allow them to create individual branches for their own project milestones/work.
#The fork is currently under my GitHub account: Bhamilton18.

===Milestone 3===
#For this portion the following steps were needed to download the GRNsight GitHub code:
#* '''git clone''' the GitHub fork created and downloaded to Atom.
#* '''cd''' into the folder that contains the cloned repository
#* '''git checkout''' the branch that is assigned to you:
#** Interaction and Integration: ''master'' was our respective branch.
# We followed the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

===Milestone 4===
#This portion of the assignment was a bit slow due to our collaboration with other groups milestones. Once they complete their respective tasks, we will begin integrating them onto the GRNsight GitHub.
#Instead, Zach and I explored the GRNsight code and worked on our team page based on the week 11 feedback from Dr. Dahlquist.

==Acknowledgments==
#For this week's assignment I collaborated with my group members, [[User:Zvanysse|Zachary Van Ysseldyk]], [[User:kwrigh35|Katie Wright]] and [[User:Emmatyrnauer|Emma Tyrnauer]] to complete individual portions of the final group project. We primarily communicated through text to clarify homework questions and update progress of the project.
#*Zach and I met in person and collaborated on formatting of the notebook page, as well as, discussed milestones.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 22:06, 13 December 2017 (PST)
==References==
LMU BioDB 2017. (2017). Week 12. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

{{Bhamilton18}}

Bhamilton18 Week 14

2017-12-14T06:06:08Z

Bhamilton18: Forgot to add signature to acknowledgments

==Electronic Lab Notebook==
This week [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked to progress the Coder portion of our Interaction and Integration section of the final project.
#To begin we had a group meeting in order to gauge the progress of each member in the group.
#Zach and I also met with Dondi in order to work on syntax for our coding part of the assignment.
#We began by trying to have the user '''right''' click on any of the genes of the GRNsight page to open any page.
#*For our purposes we used this weskit to link to the page: http://dogtime.com/dog-breeds/pug#/slide/1
#*It is important to note we did not care which website we were going to, we just wanted to link the right click to some website.
#Next, we worked on creating a simple web page, similar to our gene pages, in which the site can link to instead of the outside website source.
#*One problem we realized was happening was that Safari and Chrome believe the websites are pop-ups and therefore blocks them.
#*We have not fixed this problem yet but we have noted it.
# href: "/gene/info.html?" + $.param({symbol: gene.name}),
#* This code allows the right click to go to a generic page called info.html
#*Next the parameters goes to the gene selected and gives it's name.
#**I.e if "HOT1" is right clicked the new page will show a console.log of the gene name.
#Finally we merged the other groups work for the first integration. All went smoothly and we will be collaborating more with groups soon.
#*This merge was done through GitHub and pushed to our GitHub branch: https://github.com/bhamilton18/GRNsight

==Acknowledgements==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the D3 syntax and working through the right click problem.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 22:06, 13 December 2017 (PST)
==References==
#Get url parameter jquery Or How to Get Query String Values In js. Retrieved December 04, 2017, from https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js
#How to retrieve GET parameters from javascript? Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
#JavaScript Window Location. Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
#LMU BioDB 2017. (2017). Coder. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Coder
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
#Window.location. Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Bhamilton18}}

Lights, Camera, InterACTION!

2017-12-14T06:04:22Z

Bhamilton18: added executive summary

[[File:PugNotDrugsLogo.png|400px|thumb|right|Pugs Not Drugs Logo]]

==Team Members==
*[[user:bhamilton18|Blair Hamilton]] '''-Coder'''
*[[user:emmatyrnauer|Emma Tyrnauer]] '''-Data Analyst'''
*[[user:kwrigh35|Katie Wright]] '''-Project Manager/Quality Assurance'''
*[[user:zvanysse|Zach Van Ysseldyke]] '''-Coder'''

==File Roundup==
*Final Presentation: [[media:LCI Presentation.pdf]]
*Week 11 presentation by Blair and Zach: [[media:The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf|The Secret Startup that Saved the Worst Website in America]]
*Week 12 presentation by Emma and Katie: [[media:Genome-wide expression analysis of yeast response during exposure to 4 degrees C.pdf|Genome-wide expression analysis of yeast response during exposure to 4 degrees C]]
*Microarray data excel spreadsheet (corrected) : [[Media:Wt_Microarraydata_ET.zip]]
[[Lights, Camera, InterACTION! Deliverables]]

==Team Schedule== 
{| 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''' <s> C: PPT Presentation PM/DA: Journal Articles</s>
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' <s>C: Complete setup steps (Milestones 0-4) PM/DA: Journal Club Presentations DA: Week 8 and Week 10 edits</s>
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' <s>C: First Integration projected completion</s> <s>PM: Check in with team DA: </s>
|'''29'''
|'''30''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA:</s>
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' <s>C: Check in with groups, and further integrate as needed.</s> PM: Check in with team <s>DA: complete week 10 data analysis</s>
|'''6'''
|'''7''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA: </s>
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' <s>Final group Presentation ''2:00-4:00PM''</s>
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==
===Week 11===
====Katie - PM/QA====
For this week, I worked with [[user:emmatyrnauer|Emma]] to find papers to use as reference in our final research paper. Emma and I both found papers that are related to yeast cold shock reactions and most of them use microarray data. I am excited to read these articles more in depth as we develop our research project and paper. Further information can be found on my [[kwrigh35 Week 11|Week 11]] journal page.
#'''What worked?''' Using the three different sources was really helpful because I had never used "Web of Science" before. It was good to learn about how different these results can be, especially with tweaking the search terms a little bit.
#'''What didn't work?''' I had poor time management this week. I waited until Monday to do the majority of the work and definitely should not have done so. The rest of the project went well, however.
#'''What will I do next to fix what didn't work?''' I will plan to meet up with Emma early on in the week so we can work together on our presentation. This way I will be held accountable to get my work done earlier.

====Emma - Data Analysis====
This week Katie and I worked on the annotated bibliography (below). We chose papers that provided more information on yeast gene regulation in response to cold shock. Pub Med, Google Scholar, and Web of Science were utilized to perform basic searches using key words as well as advanced searches which helped to narrow the results. More detailed information can be found on my individual journal entry page: [[Emmatyrnauer Week 11]]. Meanwhile, Blair and Zach worked on coder journal club presentation. Construction of the group page was completed during class.
# Overall, this week went pretty smoothly; Katie and I communicated over text to determine which papers we were going to write the bibliographies for and were available to each other for any questions we had.
# There wasn't really anything that didn't work.
# Since we will be working this next week on our journal club presentation, it might be beneficial to meet in person.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:26, 13 November 2017 (PST)

====Blair - Coder====
This week Zach and I created the Powerpoint presentation about ''The secret startup that saved the worst website in America'' article. We created individual outlines of the article on our respective pages, mine is as follows: [[Bhamilton18 Week 11]]. Our presentation is linked here: [[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]
#Overall, our communication and diving up of tasks went well and smoothly. Meanwhile, Katie and Emma worked on the annotate bibliography. While I primarily worked with Zach our communication amongst group members went well and we hope to continue to do so for the future.
#Something that didn't work as well was our time management. Next time we hope to have more class time and start working earlier on our portion of the assignment.
#For the future, we will continue to communicate in person and through messaging and will work on time management by starting earlier.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 23:35, 13 November 2017 (PST)

====Zach - Coder====
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]] 
[[Zvanysse Week 11]] 
This week, Blair and I created a Powerpoint about the "Secret Startup that saved the worst website in America." We read through the article and picked out the relevant themes and main messages to put on the PowerPoint. We wrote these themes and summaries out on our individual Journals. Then, we collaborated and made our PowerPoint.
#'''Things that went well:''' Blair and I's communication was very strong and we knew exactly what was going on with one another. We knew when we were going to meet up and what was expected for each of us.
#'''Things that didn't go well:''' Blair and I missed the mark on our time management. We did not expect this assignment to take this long. Next time, we will make sure to start on assignments earlier.
#Like I said above, we will plan out exact times earlier on in the week that we can meet up
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 23:44, 13 November 2017 (PST) 

===Week 12===
====Katie - PM/QA====
Emma and I worked on our presentation on "Genome-wide expression analysis of yeast response during exposure to 4 degrees C," details of which can be found on my [[kwrigh35 Week 12|Week 12]] page. The presentation can be found in the "file roundup" section of this page.
#'''What worked?'''Emma and I met up outside of class to work on the assignment, which was really helpful.
#'''What didn't work?'''I underestimated to the time it would take to find 10 terms that I didn't know before reading the paper. It was hard to find 10, so I resorted to picking terms that I knew but wanted to know more about. It was also difficult to find definitions for some of these words, because some of them weren't in biological dictionaries.
#'''What will I do next to fix what didn't work?'''I should start work on the assignment before the weekend begins. That way, I don't have to spend the majority of my Monday afternoon/evening on the project. It is better to be able to come back to a project several times, and each time have "fresh" eyes.

====Emma - Data Analysis====
This week I made all the corrections listed on the talk page of my user page for both [[Emmatyrnauer Week 8]] and [[Emmatyrnauer Week 10]]. This included corrections to the excel files, stem analysis, electronic notebooks, analysis of log fold changes and p values, and the acknowledgements section. Following the completion of fixing the errors in the excel file, I emailed Dr. Dahlquist to ascertain that I completed the analysis correctly. For the individual assignment this week, Katie and I met up to work on our journal club presentation of the paper that we were assigned (can be accessed on my individual journal page, [[Emmatyrnauer Week 12]]. We divided up what portions we would be responsible for and have planned to meet up before class tomorrow to practice. The paper we were assigned is: Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. The powerpoint presentation and updated excel file can be accessed above under "File Roundup."
#'''What worked well:''' It was very helpful to meet up in person with Katie to begin working on the powerpoint before separating everything out.
#'''What didn't worked well:''' This week I had so much to do including fixing both week 8 and week 10 individual pages and redoing stem because of the mistake I made in excel. I could have asked for an extension on the excel files to allow for more time to work on the presentation. I could have also been in better communication with Blair and Zach this week.
#'''What will we do to fix what didn't work?''' I will communicate more with the professors. Sitting down together with my group will also help to get us all on the same page for the future weeks.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:03, 20 November 2017 (PST)

====Blair - Coder====
As mentioned on my electronic notebook, [[Bhamilton18 Week 12]], this week's assignment Zachary Van Ysseldyk and I worked on the Coder Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project. Zach and I met in person to collaborate on formatting of the team page, individual journal pages and project progress.
#'''What worked well:''' Zach and I worked on better time management as well as expectations for the assignment. We were able to communicate without any hiccups, and meeting up in person was ideal for clarifying issues.
#'''What didn't worked well:''' We were unsure of our progress in the project as our understanding of milestone 4 meant we needed to wait this week on others.
#'''What will we do to fix what didn't work?''' Checking in with our project teams/coders will help us understand how they are doing, as well as how our own progression is lining up.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 19:15, 20 November 2017 (PST)
====Zach - Coder====
This week, Blair and I worked on the coder milestones. We will work on integrating the actual other team's parts as they start to finish. We also collaborated with Emma and Katie to make sure that we were on the same page. 
[[Zvanysse Week 12]] 
#'''Things that went well:''' we were better about our time management as well as we communicated well. We met up together periodically to make sure that we were on the same page.
#'''Things that didn't go well:''' We were a little confused on how to go about the project for our milestone considering that it was more of a waiting game this week rather than actual integration. So, we didn't really know how to quantify our progress.
#'''What we will do to fix it:''' We maybe should have collaborated with the other teams a little bit more to be able and gauge how their projects are coming along.

===Week 14===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I worked on completing the week 10 analysis and visualized a gene regulatory network for the wild type strain with GRNsight. All of the steps I took and files used can be found on my individual page: [[Emmatyrnauer Week 14]].
#'''Things that went well:''' It was nice that I had already completed the week 8 and week 10 corrections so that I could just focus on completing the data analysis. I went in to talk to Dr. Dahlquist with issues that I was having during analysis of the microarray data. This allowed for faster and accurate completion of the analysis. I was also able to contact the data analysis guild with any questions that I had.
#'''Things that didn't go well:''' Everything went pretty smoothly this week; it was very helpful having work time in class to complete my last milestone.
#'''What we will do to fix it:''' For next week, I will continue to work with the data analyst guild to complete final individual tasks for the project. I will also be collaborating more with my group members to pull together the final deliverables, paper, and presentation.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:31, 4 December 2017 (PST)

====Blair - Coder====
This week Zach and I worked on the first integration of the website and added a right click feature to each gene. We met in person and text messaged each other. As mentioned in my electronic notebook, [[Bhamilton18 Week 14]], we found online resources to add this right click feature as well as collaborate with Dr. Dionisio for syntax problems. This week Emma focused on progressing with data analysis for the gene wild type and then Katie made sure all groups were giving us their deliverables.
#'''Things that went well:''' Collaboration with other groups was productive and went smoothly. Having Dr. Dionisio as a resource has been very helpful and quickened the process.
#'''Things that didn't go well:''' Working in D3 syntax has been difficult to progress in certain deliverables.
#'''What we will do to fix it:''' In order to fix this problem, Zach and I hope to work closely with Dr. Dionisio finding external resources and fixing small errors.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 21:25, 4 December 2017 (PST)
====Zach - Coder====
This week Blair and I worked on the first integration by merging through github as well as working on the right click function. This function enabled us to right click and automatically link the gene that was clicked on to that particular gene page. We connected by texting as well as meeting up in person before committing our week's work to make sure that we were on the same page. We mentioned this on my electronic notebook, [[Zvanysse Week 14]]. We collaborated with Dr. Dionisio to work out some of the D3 technical syntax problems that came about. Emma worked on progressing on the data analysis for the gene wild type and Katie make sure that everyone was on task.
#'''What went well:''' Our communication and procrastination was overall much better. Collaborating with other teams went smoothly and connecting with Dr. Dionisio for syntax went well as the problem was diagnosed soon after it became about.
#'''What Didn't go well:''' Working with D3 was a little difficult because the syntax ultimately changed for the API. This was unforeseen so it was a little frustrating.
#'''How will we fix this:''' When it comes to syntax problems, we will be more in communication with Dr. Dionisio 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 21:36, 4 December 2017 (PST)

===Week 15===
====Katie - PM/QA====
====Emma - Data Analysis====
====Blair - Coder====
For the final week of the project [[User:Zvanysse|Zach]] and I worked heavy on the integration portion of the coding. We inputed the data into the overall info.html page, referenced the gene ids of the following databases: NCBI, SGD, UniProt, JASPAR and Ensembl, and finally met with each coding groups to finalize the final pull of code from everyone. More details on the code and final project can be read on my electronic lab notebook: [[Bhamilton18 Week 15]]. For the final project deliverables, Katie, Emma, Zach and I met twice to collaborate on the presentation, read over our slides and add in details/pictures. Lastly, we communicated through text message and google slides/docs to complete the powerpoint and final paper.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 22:04, 13 December 2017 (PST)
====Zach - Coder====

==Bibliography==
===Paper 1===
Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. ''Cryobiology'', 46(3), 230-237.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212
* PubMed Central: not available
* Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
* Publisher Full Text (PDF): https://electra.lmu.edu:3555/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=4c9b7cc0-c775-11e7-af71-00000aab0f26&acdnat=1510469407_3e02bee4266fd6a211ea3f6e27b460cf
* Copyright: 2003 by Science Direct; article is not Open Access
* Publisher: Elsevier Science
* Availability: online at www.sciencedirect.com
* Did LMU pay a fee for this article: yes

===Paper 2===
Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. ''Extremophiles'', 10(2), 117-128.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome-wide+expression+analysis+of+yeast+response+during+exposure+to+4+degrees+C
* PubMed Central: not available
* Publisher Full Text (HTML): https://electra.lmu.edu:2529/article/10.1007/s00792-005-0480-1
* Publisher Full Text (PDF): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=16254683
* Copyright: 2005 by Springer-Verlag; article is not Open Access
* Publisher: Springer-Verlag
* Availability: online
* Did LMU pay a fee for this article: yes

===Paper 3===
Becerra, M., Lombardia, L. J., González‐Siso, M. I., Rodríguez‐Belmonte, E., Hauser, N. C., & Cerdán, M. E. (2003). Genome‐wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and functional genomics, 4(4), 366-375.

'''PubMed Abstract:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/

'''PubMed Central:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf

'''Publisher Full Text (HTML):''' unavailable

'''Publisher Full Text (PDF):''' http://downloads.hindawi.com/journals/ijg/2003/175356.pdf

'''Copyright:''' Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

'''Publisher:''' Hindawi Publishing Corporation

'''Availability:''' Open access

'''Did LMU pay a fee for this article:''' no

===Paper 4===
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.

'''PubMed Abstract: ''' https://www.ncbi.nlm.nih.gov/pubmed/?term=Comprehensive+expression+analysis+of+time-dependent+genetic+responses+in+yeast+cells+to+low+temperature

'''PubMed Central: ''' not available

'''Publisher Full Text (HTML): ''' http://www.jbc.org/content/277/51/50015.long

'''Publisher Full Text (PDF): ''' http://www.jbc.org/content/277/51/50015.full.pdf

'''Copyright: ''' "Other parties are welcome to copy, distribute, transmit and adapt the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above." from http://www.jbc.org/site/misc/Copyright_Permission.xhtml

'''Publisher: ''' American Society for Biochemistry and Molecular Biology

'''Availability: '''All articles from this journal are free 1 year after publishing.

'''Did LMU pay a fee for this article:''' No.

==Acknowledgments==
#Our group collaborates on this page each week filling out our respective team journal assignments and project updates.
#*WE have a group chat to communicate problems, questions and ideas for our weekly assignments/milestones.
#We utilized the Calendar outline from the [[JASPAR the Friendly Ghost]] page, but changed the milestone/tasks due.

==References==
*Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup- saved-healthcare-gov-the-worst-website-in-america/397784/
*Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf

{{template:Pugs Not Drugs}}

{{GRNsight Gene Page Project Links}}

Template:Bhamilton18 Contact Info

2017-12-14T05:56:46Z

Bhamilton18: Added final project to template

{| class="wikitable" style="Background: cream"
|-
!style="background: coral;color:white"| Category !!style="background: coral;color:white"| Links
|-
| '''User Page''' ||style="width:700px"|[[User:Bhamilton18| Blair Hamilton]]
|-
| '''Weekly Assignments''' ||style="width:700px" |[[Bhamilton18 Week 2]] &emsp; [[Bhamilton18 Week 3]] &emsp; [[Bhamilton18 Week 4]]&emsp; [[Animal QTL]]&emsp; [[Bhamilton18 Week 6]]&emsp; [[Bhamilton18 Week 7]]&emsp; [[Bhamilton18 Week 8]]&emsp; [[Bhamilton18 Week 9]]&emsp; [[Bhamilton18 Week 10]]&emsp; [[Bhamilton18 Week 11]]&emsp; [[Bhamilton18 Week 12]]&emsp; [[Bhamilton18 Week 14]]&emsp; [[Bhamilton18 Week 15]]
|-
|'''Weekly Assignment Instructions'''||style="width:700px"| [[Week 1]] &emsp; [[Week 2]] &emsp; [[Week 3]] &emsp; [[Week 4]] &emsp; [[Week 5]] &emsp; [[Week 6]] &emsp; [[Week 7]] &emsp; [[Week 8]] &emsp; [[Week 9]] &emsp; [[Week 10]] &emsp; [[Week 11]] &emsp; [[Week 12]] &emsp; [[Week 14]] &emsp; [[Week 15]]
|-
| '''Class Journals''' ||style="width:700px"| [[Class Journal Week 1]] &emsp; [[Class Journal Week 2]] &emsp; [[Class Journal Week 3]] &emsp; [[Class Journal Week 4]] &emsp; [[Class Journal Week 5]] &emsp; [[Class Journal Week 6]] &emsp; [[Class Journal Week 7]] &emsp; [[Class Journal Week 8]] &emsp; [[Class Journal Week 9]] &emsp; [[Class Journal Week 10]]
|-
|'''Final Project''' ||style="width:700px"| [[Lights, Camera, InterACTION!]]&emsp; [[Lights, Camera, InterACTION! Deliverables]]
|}

[[Category:Journal Entry]]

Bhamilton18 Week 15

2017-12-14T05:50:30Z

Bhamilton18: fixed typos

==Coding Updates==
#This week Zach and I focused on major integration of the JASPAR, Gene Database APIs and Page Design teams.
#Due to some communication issues of Week 14, Zach and I were backtracked on certain integrations with other groups, but quickly made up for lost time.
#*These backtracks include: gene id syntax and api referencing, as well as page-design collaboration on where classes should go.
#Our task for this week was to add IDs from: NCBI, SGD, Ensembl, Uniprot and JASPAR to the top of the gene page, as well as input the data onto the info.html page.
#*This was completed with by taking the Gene Database APIs and JASPAR API calls and creating a link id on the info.js file.
#*Currently there are IDs for all the databases and data that was requested by the biologists.
#By communicating with Dr. Dionisio we found the correct ID format to reference the info.html file as well as the api.js file.
#*'''This looks as follows:'''
#*<code>var sgdHrefTemplate = "https://www.yeastgenome.org/locus/"; </code>
#**When the template is then used as the URL foundation for other data entries.
#*<code>var sgdId = gene.sgd.sgdID;</code>
#**When the ID is used it is referencing the API calls from the Gene Database API code, located in api.js.
#*<code>$(".sgd-link").text(sgdId).attr({ href: sgdHrefTemplate + sgdId });</code>
#**This references jquery in which is grabs the info.html file class and puts in text as well as the data from the databases.
#Each ID was created and required a few git pull commands as the other teams needed to fix api calls and retrieve the correct data.
#*As of today, December 13 2017, the information is pulling all correct data and is waiting on a few data points form the API team.
#*This is how it is displayed for HMO1:
#*[[File:GeneIDs.png|500px|thumb|center|Gene ID look for HMO1]]
#After the IDs had been created Zach and I focused on using the similar format for all other p-tagged classes that required data.
#The reason we clarify p-tag was because for the gene frequency matrix and sequence logo the syntax was difference as they required an image and additional code to produce a table.
#*While trying to create a table for the frequency matrix our team ran into a few bumps in the code and required Dr. Dionisio's help, and Eddie B's help to format a table.
#*The table now uses multiple for-loops to integrate through the matrix elements as the sizing per gene changes for every gene. Anywhere from 0-15 elements.
#*'''This is the code for the for loop, specifically the A matrix portion:'''
#**<code>var frequencyMatrix = gene.jaspar.frequencyMatrix;</code>
#**<code>var a = "";</code>
#**<code>for (var i = 0; i < frequencyMatrix.A.length; i++) {</code>
#**<code>a += "<td>" + frequencyMatrix.A[i] + "</td>";</code>
#**<code>}</code>
#**<code>$(".frequencyOfA").append($(a));</code>
#*An additional hurtle that needed jumping over was the sequence logo image. Through Dr.Dionisio's help, we created a link between the image src file and the JASPAR API call. Talking with Eddie B. about how his call retrieves the image URL was very helpful in retrieving this information.
#*'''This can be seen here:'''
#**<code>var sequenceLogo = gene.jaspar.sequenceLogo;</code>
#**<code>$(".sequenceLogo").attr({ src : sequenceLogo });</code>
#***The biggest difference from above is the src instead of href portion of the attributes.
#Here is how the data is displayed on the page for ASH1:
#*[[File:MatrixPic.png|500px|thumb|center|Fequency Matrix and Sequence Logo for ASH1 Gene]]
#After all the data had place holders, actual data or images, the final step was to create an appealing layout of the information. Through collaboration with the Page-Design team our ideas and the biologists hopes were implemented and hope to be complete by December 14.
#Below is the current look of the page, using HOT1 gene as the example:
#*[[File:Infohtmlpic.png|600px|thumb|center|GRNsight Gene Page for HOT1]]

==Team Deliverable Progress==
This week Katie, Zach and I were able to meet up twice in order to finalize our project presentation details. We practiced our respective parts and discussed our progress within our team tasks. As noted above the Coders had quite a few tasks to complete, and the Data Analyst and Project Manager were able to collaborate and help each other of the data progress and outputs. Our presentation was completed on Monday night. We communicated through text message, in person and created a google slide deck in order to collaborate off site. Zach and I inputed images, titles and text into the coding portion of the assignment as well as give flow chart details to Katie to update the presentation.

As for the final deliverables, the Coders will be doing a final pull and push request December 14 and potentially the 15th if any major changes need to be made. Our team will be communicating via text message and google docs in order to complete the paper portion of the assignment. Zach and I will be discussing our respective parts of the project and will divide the work load for the paper.

Our deliverables can be seen here: [[Lights, Camera, InterACTION! Deliverables|LCI! Deliverables]]

==Acknowledgments==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We met in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the id syntax and class referencing portions.
#Interaction and Integration team worked with JASPAR team to check in about the frequency matrix and sequence logo syntax.
#Collaborated with [[User:ebachour|Eddie Bachoura]] on creating a table/for-loop for the frequency matrix portion of the info.html page.
#Collaborated with [[User:cazinge|Eddie Azinge]] on the gene name referencing between pages. For example, to get the gene name to appear at the top of the info.html page, Eddie A. helped by showing me how to attach an id to the name I wanted and then reference it in the info.js file.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 12:58, 11 December 2017 (PST)

==References==

LMU BioDB 2017. (2017). Deliverables. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

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

{{Bhamilton18}}

Bhamilton18 Week 15

2017-12-14T05:49:40Z

Bhamilton18: Added one more screenshot of GRNsight page

==Coding Updates==
#This week Zach and I focused on major integration of the JASPAR, Gene Database APIs and Page Design teams.
#Due to some communication issues of Week 14, Zach and I were backtracked on certain integrations with other groups, but quickly made up for lost time.
#*These backtracks include: gene id syntax and api referencing, as well as page-design collaboration on where classes should go.
#Our task for this week was to add IDs from: NCBI, SGD, Ensembl, Uniprot and JASPAR to the top of the gene page, as well as input the data onto the info.html page.
#*This was completed with by taking the Gene Database APIs and JASPAR API calls and creating a link id on the info.js file.
#*Currently there are IDs for all the databases and data that was requested by the biologists.
#By communicating with Dr. Dionisio we found the correct ID format to reference the info.html file as well as the api.js file.
#*'''This looks as follows:'''
#*<code>var sgdHrefTemplate = "https://www.yeastgenome.org/locus/"; </code>
#**When the template is then used as the URL foundation for other data entries.
#*<code>var sgdId = gene.sgd.sgdID;</code>
#**When the ID is used it is referencing the API calls from the Gene Database API code, located in api.js.
#*<code>$(".sgd-link").text(sgdId).attr({ href: sgdHrefTemplate + sgdId });</code>
#**This references jquery in which is grabs the info.html file class and puts in text as well as the data from the databases.
#Each ID was created and required a few git pull commands as the other teams needed to fix api calls and retrieve the correct data.
#*As of today, December 13 2017, the information is pulling all correct data and is waiting on a few data points form the API team.
#*This is how it is displayed for HMO1:
#*[[File:GeneIDs.png|500px|thumb|center|Gene ID look for HMO1]]
#After the IDs had been created Zach and I focused on using the similar format for all other p-tagged classes that required data.
#The reason we clarify p-tag was because for the gene frequency matrix and sequence logo the syntax was difference as they required an image and additional code to produce a table.
#*While trying to create a table for the frequency matrix our team ran into a few bumps in the code and required Dr. Dionisio's help, and Eddie B's help to format a table.
#*The table now uses multiple for-loops to integrate through the matrix elements as the sizing per gene changes for every gene. Anywhere from 0-15 elements.
#*'''This is the code for the for loop, specifically the A matrix portion:'''
#**<code>var frequencyMatrix = gene.jaspar.frequencyMatrix;</code>
#**<code>var a = "";</code>
#**<code>for (var i = 0; i < frequencyMatrix.A.length; i++) {</code>
#**<code>a += "<td>" + frequencyMatrix.A[i] + "</td>";</code>
#**<code>}</code>
#**<code>$(".frequencyOfA").append($(a));</code>
#*An additional hurtle that needed jumping over was the sequence logo image. Through Dr.Dionisio's help, we created a link between the image src file and the JASPAR API call. Talking with Eddie B. about how his call retrieves the image URL was very helpful in retrieving this information.
#*'''This can be seen here:'''
#**<code>var sequenceLogo = gene.jaspar.sequenceLogo;</code>
#**<code>$(".sequenceLogo").attr({ src : sequenceLogo });</code>
#***The biggest difference from above is the src instead of href portion of the attributes.
#Here is how the data is displayed on the page for ASH1:
#*[[File:MatrixPic.png|500px|thumb|center|Fequency Matrix and Sequence Logo for ASH1 Gene]]
#After all the data had place holders, actual data or images, the final step was to create an appealing layout of the information. Through collaboration with the Page-Design team our ideas and the biologists hopes were implemented and hope to be complete by December 14.
#Below is the current look of the page, using HOT1 gene as the example:
#*[[File:Infohtmlpic.png|600px|thumb|center|GRNsight Gene Page for HOT1]]

==Team Deliverable Progress==
This week Katie, Zach and I were able to meet up twice in order to finalize our project presentation details. We practiced our respective parts and discussed our progress within our team tasks. As noted above the Coders had quite a few tasks to complete, and the Data Analyst and Project Manager were able to collaborate and help each other of the data progress and outputs. Our presentation was completed on Monday night. We communicated through text message, in person and created a google slide deck in order to collaborate off site. Zach and I inputed images, titles and text into the coding portion of the assignment as well as give flow chart details to Katie to update the presentation.

As for the final deliverables, the Coders will be doing a final pull and push request December 14 and potential the 15th if any major changes need to be made. Our team will be communicating via text message and google docs in order to complete the paper portion of the assignment. Zach and I will be discussing our respective parts of the project and will divide the work load for the paper.

Our deliverables can be seen here: [[Lights, Camera, InterACTION! Deliverables|LCI! Deliverables]]

==Acknowledgments==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We met in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the id syntax and class referencing portions.
#Interaction and Integration team worked with JASPAR team to check in about the frequency matrix and sequence logo syntax.
#Collaborated with [[User:ebachour|Eddie Bachoura]] on creating a table/for-loop for the frequency matrix portion of the info.html page.
#Collaborated with [[User:cazinge|Eddie Azinge]] on the gene name referencing between pages. For example, to get the gene name to appear at the top of the info.html page, Eddie A. helped by showing me how to attach an id to the name I wanted and then reference it in the info.js file.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 12:58, 11 December 2017 (PST)

==References==

LMU BioDB 2017. (2017). Deliverables. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

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

{{Bhamilton18}}

File:GeneIDs.png

2017-12-14T05:47:32Z

Bhamilton18: Gene ID look for HMO1

Gene ID look for HMO1

Bhamilton18 Week 15

2017-12-14T05:45:52Z

Bhamilton18: Added screenshots and code examples

==Coding Updates==
#This week Zach and I focused on major integration of the JASPAR, Gene Database APIs and Page Design teams.
#Due to some communication issues of Week 14, Zach and I were backtracked on certain integrations with other groups, but quickly made up for lost time.
#*These backtracks include: gene id syntax and api referencing, as well as page-design collaboration on where classes should go.
#Our task for this week was to add IDs from: NCBI, SGD, Ensembl, Uniprot and JASPAR to the top of the gene page, as well as input the data onto the info.html page.
#*This was completed with by taking the Gene Database APIs and JASPAR API calls and creating a link id on the info.js file.
#*Currently there are IDs for all the databases and data that was requested by the biologists.
#By communicating with Dr. Dionisio we found the correct ID format to reference the info.html file as well as the api.js file.
#*'''This looks as follows:'''
#*<code>var sgdHrefTemplate = "https://www.yeastgenome.org/locus/"; </code>
#**When the template is then used as the URL foundation for other data entries.
#*<code>var sgdId = gene.sgd.sgdID;</code>
#**When the ID is used it is referencing the API calls from the Gene Database API code, located in api.js.
#*<code>$(".sgd-link").text(sgdId).attr({ href: sgdHrefTemplate + sgdId });</code>
#**This references jquery in which is grabs the info.html file class and puts in text as well as the data from the databases.
#Each ID was created and required a few git pull commands as the other teams needed to fix api calls and retrieve the correct data.
#*As of today, December 13 2017, the information is pulling all correct data and is waiting on a few data points form the API team.
#After the IDs had been created Zach and I focused on using the similar format for all other p-tagged classes that required data.
#The reason we clarify p-tag was because for the gene frequency matrix and sequence logo the syntax was difference as they required an image and additional code to produce a table.
#*While trying to create a table for the frequency matrix our team ran into a few bumps in the code and required Dr. Dionisio's help, and Eddie B's help to format a table.
#*The table now uses multiple for-loops to integrate through the matrix elements as the sizing per gene changes for every gene. Anywhere from 0-15 elements.
#*'''This is the code for the for loop, specifically the A matrix portion:'''
#**<code>var frequencyMatrix = gene.jaspar.frequencyMatrix;</code>
#**<code>var a = "";</code>
#**<code>for (var i = 0; i < frequencyMatrix.A.length; i++) {</code>
#**<code>a += "<td>" + frequencyMatrix.A[i] + "</td>";</code>
#**<code>}</code>
#**<code>$(".frequencyOfA").append($(a));</code>
#*An additional hurtle that needed jumping over was the sequence logo image. Through Dr.Dionisio's help, we created a link between the image src file and the JASPAR API call. Talking with Eddie B. about how his call retrieves the image URL was very helpful in retrieving this information.
#*'''This can be seen here:'''
#**<code>var sequenceLogo = gene.jaspar.sequenceLogo;</code>
#**<code>$(".sequenceLogo").attr({ src : sequenceLogo });</code>
#***The biggest difference from above is the src instead of href portion of the attributes.
#Here is how the data is displayed on the page for ASH1:
#*[[File:MatrixPic.png|500px|thumb|center|Fequency Matrix and Sequence Logo for ASH1 Gene]]
#After all the data had place holders, actual data or images, the final step was to create an appealing layout of the information. Through collaboration with the Page-Design team our ideas and the biologists hopes were implemented and hope to be complete by December 14.
#Below is the current look of the page, using HOT1 gene as the example:
#*[[File:Infohtmlpic.png|600px|thumb|center|GRNsight Gene Page for HOT1]]

==Team Deliverable Progress==
This week Katie, Zach and I were able to meet up twice in order to finalize our project presentation details. We practiced our respective parts and discussed our progress within our team tasks. As noted above the Coders had quite a few tasks to complete, and the Data Analyst and Project Manager were able to collaborate and help each other of the data progress and outputs. Our presentation was completed on Monday night. We communicated through text message, in person and created a google slide deck in order to collaborate off site. Zach and I inputed images, titles and text into the coding portion of the assignment as well as give flow chart details to Katie to update the presentation.

As for the final deliverables, the Coders will be doing a final pull and push request December 14 and potential the 15th if any major changes need to be made. Our team will be communicating via text message and google docs in order to complete the paper portion of the assignment. Zach and I will be discussing our respective parts of the project and will divide the work load for the paper.

Our deliverables can be seen here: [[Lights, Camera, InterACTION! Deliverables|LCI! Deliverables]]

==Acknowledgments==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We met in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the id syntax and class referencing portions.
#Interaction and Integration team worked with JASPAR team to check in about the frequency matrix and sequence logo syntax.
#Collaborated with [[User:ebachour|Eddie Bachoura]] on creating a table/for-loop for the frequency matrix portion of the info.html page.
#Collaborated with [[User:cazinge|Eddie Azinge]] on the gene name referencing between pages. For example, to get the gene name to appear at the top of the info.html page, Eddie A. helped by showing me how to attach an id to the name I wanted and then reference it in the info.js file.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 12:58, 11 December 2017 (PST)

==References==

LMU BioDB 2017. (2017). Deliverables. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

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

{{Bhamilton18}}

File:MatrixPic.png

2017-12-14T05:44:40Z

Bhamilton18: Frequency Matrix and sequence logo

Frequency Matrix and sequence logo

File:Infohtmlpic.png

2017-12-14T05:41:48Z

Bhamilton18: GRNSight gene page look

GRNSight gene page look

Bhamilton18 Week 15

2017-12-14T05:25:35Z

Bhamilton18: Updated notebook for final deliverables and coding

==Coding Updates==
#This week Zach and I focused on major integration of the JASPAR, Gene Database APIs and Page Design teams.
#Due to some communication issues of Week 14, Zach and I were backtracked on certain integrations with other groups, but quickly made up for lost time.
#*These backtracks include: gene id syntax and api referencing, as well as page-design collaboration on where classes should go.
#Our task for this week was to add IDs from: NCBI, SGD, Ensembl, Uniprot and JASPAR to the top of the gene page, as well as input the data onto the info.html page.
#*This was completed with by taking the Gene Database APIs and JASPAR API calls and creating a link id on the info.js file.
#*Currently there are IDs for all the databases and data that was requested by the biologists.
#By communicating with Dr. Dionisio we found the correct ID format to reference the info.html file as well as the api.js file.
#*'''This looks as follows:'''
#*<code>var sgdHrefTemplate = "https://www.yeastgenome.org/locus/"; </code>
#**When the template is then used as the URL foundation for other data entries.
#*<code>var sgdId = gene.sgd.sgdID;</code>
#**When the ID is used it is referencing the API calls from the Gene Database API code, located in api.js.
#*<code>$(".sgd-link").text(sgdId).attr({ href: sgdHrefTemplate + sgdId });</code>
#**This references jquery in which is grabs the info.html file class and puts in text as well as the data from the databases.
#Each ID was created and required a few git pull commands as the other teams needed to fix api calls and retrieve the correct data.
#*As of today, December 13 2017, the information is pulling all correct data and is waiting on a few data points form the API team.
#After the IDs had been create Zach and I focused on using the similar format for all other p-tagged classes that required data.
#The reason we clarify p-tag was because for the gene frequency matrix and sequence logo the syntax was difference as they required an image and additional code to produce a table.
#*While trying to create a table for the frequency matrix our team ran into a few bumps in the code and required Dr. Dionisio's help, and Eddie B's help to format a table.
#*The table now uses multiple for-loops to integrate through the matrix elements as the sizing per gene changes for every gene. Anywhere from 0-15 elements.
#*An additional hurtle that needed jumping over was the sequence logo image. Through Dr.Dionisio's help, we created a link between the image src file and the JASPAR API call. Talking with Eddie B. about how his call retrieves the image URL was very helpful in retrieving this information.
#After all the data had place holders, actual data or images, the final step was to create an appealing layout of the information. Through collaboration with the Page-Design team our ideas and the biologists hopes were implemented and hope to be complete by December 14.

==Team Deliverable Progress==
This week Katie, Zach and I were able to meet up twice in order to finalize our project presentation details. We practiced our respective parts and discussed our progress within our team tasks. As noted above the Coders had quite a few tasks to complete, and the Data Analyst and Project Manager were able to collaborate and help each other of the data progress and outputs. Our presentation was completed on Monday night. We communicated through text message, in person and created a google slide deck in order to collaborate off site. Zach and I inputed images, titles and text into the coding portion of the assignment as well as give flow chart details to Katie to update the presentation.

As for the final deliverables, the Coders will be doing a final pull and push request December 14 and potential the 15th if any major changes need to be made. Our team will be communicating via text message and google docs in order to complete the paper portion of the assignment. Zach and I will be discussing our respective parts of the project and will divide the work load for the paper.

==Acknowledgments==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We met in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the id syntax and class referencing portions.
#Interaction and Integration team worked with JASPAR team to check in about the frequency matrix and sequence logo syntax.
#Collaborated with [[User:ebachour|Eddie Bachoura]] on creating a table/for-loop for the frequency matrix portion of the info.html page.
#Collaborated with [[User:cazinge|Eddie Azinge]] on the gene name referencing between pages. For example, to get the gene name to appear at the top of the info.html page, Eddie A. helped by showing me how to attach an id to the name I wanted and then reference it in the info.js file.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 12:58, 11 December 2017 (PST)

==References==

LMU BioDB 2017. (2017). Deliverables. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

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

{{Bhamilton18}}

Lights, Camera, InterACTION!

2017-12-14T04:55:39Z

Bhamilton18: added strikeout to final presentation

[[File:PugNotDrugsLogo.png|400px|thumb|right|Pugs Not Drugs Logo]]

==Team Members==
*[[user:bhamilton18|Blair Hamilton]] '''-Coder'''
*[[user:emmatyrnauer|Emma Tyrnauer]] '''-Data Analyst'''
*[[user:kwrigh35|Katie Wright]] '''-Project Manager/Quality Assurance'''
*[[user:zvanysse|Zach Van Ysseldyke]] '''-Coder'''

==File Roundup==
*Final Presentation: [[media:LCI Presentation.pdf]]
*Week 11 presentation by Blair and Zach: [[media:The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf|The Secret Startup that Saved the Worst Website in America]]
*Week 12 presentation by Emma and Katie: [[media:Genome-wide expression analysis of yeast response during exposure to 4 degrees C.pdf|Genome-wide expression analysis of yeast response during exposure to 4 degrees C]]
*Microarray data excel spreadsheet (corrected) : [[Media:Wt_Microarraydata_ET.zip]]
[[Lights, Camera, InterACTION! Deliverables]]

==Team Schedule== 
{| 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''' <s> C: PPT Presentation PM/DA: Journal Articles</s>
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' <s>C: Complete setup steps (Milestones 0-4) PM/DA: Journal Club Presentations DA: Week 8 and Week 10 edits</s>
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' <s>C: First Integration projected completion</s> <s>PM: Check in with team DA: </s>
|'''29'''
|'''30''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA:</s>
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' <s>C: Check in with groups, and further integrate as needed.</s> PM: Check in with team <s>DA: complete week 10 data analysis</s>
|'''6'''
|'''7''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA: </s>
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' <s>Final group Presentation ''2:00-4:00PM''</s>
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==
===Week 11===
====Katie - PM/QA====
For this week, I worked with [[user:emmatyrnauer|Emma]] to find papers to use as reference in our final research paper. Emma and I both found papers that are related to yeast cold shock reactions and most of them use microarray data. I am excited to read these articles more in depth as we develop our research project and paper. Further information can be found on my [[kwrigh35 Week 11|Week 11]] journal page.
#'''What worked?''' Using the three different sources was really helpful because I had never used "Web of Science" before. It was good to learn about how different these results can be, especially with tweaking the search terms a little bit.
#'''What didn't work?''' I had poor time management this week. I waited until Monday to do the majority of the work and definitely should not have done so. The rest of the project went well, however.
#'''What will I do next to fix what didn't work?''' I will plan to meet up with Emma early on in the week so we can work together on our presentation. This way I will be held accountable to get my work done earlier.

====Emma - Data Analysis====
This week Katie and I worked on the annotated bibliography (below). We chose papers that provided more information on yeast gene regulation in response to cold shock. Pub Med, Google Scholar, and Web of Science were utilized to perform basic searches using key words as well as advanced searches which helped to narrow the results. More detailed information can be found on my individual journal entry page: [[Emmatyrnauer Week 11]]. Meanwhile, Blair and Zach worked on coder journal club presentation. Construction of the group page was completed during class.
# Overall, this week went pretty smoothly; Katie and I communicated over text to determine which papers we were going to write the bibliographies for and were available to each other for any questions we had.
# There wasn't really anything that didn't work.
# Since we will be working this next week on our journal club presentation, it might be beneficial to meet in person.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:26, 13 November 2017 (PST)

====Blair - Coder====
This week Zach and I created the Powerpoint presentation about ''The secret startup that saved the worst website in America'' article. We created individual outlines of the article on our respective pages, mine is as follows: [[Bhamilton18 Week 11]]. Our presentation is linked here: [[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]
#Overall, our communication and diving up of tasks went well and smoothly. Meanwhile, Katie and Emma worked on the annotate bibliography. While I primarily worked with Zach our communication amongst group members went well and we hope to continue to do so for the future.
#Something that didn't work as well was our time management. Next time we hope to have more class time and start working earlier on our portion of the assignment.
#For the future, we will continue to communicate in person and through messaging and will work on time management by starting earlier.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 23:35, 13 November 2017 (PST)

====Zach - Coder====
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]] 
[[Zvanysse Week 11]] 
This week, Blair and I created a Powerpoint about the "Secret Startup that saved the worst website in America." We read through the article and picked out the relevant themes and main messages to put on the PowerPoint. We wrote these themes and summaries out on our individual Journals. Then, we collaborated and made our PowerPoint.
#'''Things that went well:''' Blair and I's communication was very strong and we knew exactly what was going on with one another. We knew when we were going to meet up and what was expected for each of us.
#'''Things that didn't go well:''' Blair and I missed the mark on our time management. We did not expect this assignment to take this long. Next time, we will make sure to start on assignments earlier.
#Like I said above, we will plan out exact times earlier on in the week that we can meet up
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 23:44, 13 November 2017 (PST) 

===Week 12===
====Katie - PM/QA====
Emma and I worked on our presentation on "Genome-wide expression analysis of yeast response during exposure to 4 degrees C," details of which can be found on my [[kwrigh35 Week 12|Week 12]] page. The presentation can be found in the "file roundup" section of this page.
#'''What worked?'''Emma and I met up outside of class to work on the assignment, which was really helpful.
#'''What didn't work?'''I underestimated to the time it would take to find 10 terms that I didn't know before reading the paper. It was hard to find 10, so I resorted to picking terms that I knew but wanted to know more about. It was also difficult to find definitions for some of these words, because some of them weren't in biological dictionaries.
#'''What will I do next to fix what didn't work?'''I should start work on the assignment before the weekend begins. That way, I don't have to spend the majority of my Monday afternoon/evening on the project. It is better to be able to come back to a project several times, and each time have "fresh" eyes.

====Emma - Data Analysis====
This week I made all the corrections listed on the talk page of my user page for both [[Emmatyrnauer Week 8]] and [[Emmatyrnauer Week 10]]. This included corrections to the excel files, stem analysis, electronic notebooks, analysis of log fold changes and p values, and the acknowledgements section. Following the completion of fixing the errors in the excel file, I emailed Dr. Dahlquist to ascertain that I completed the analysis correctly. For the individual assignment this week, Katie and I met up to work on our journal club presentation of the paper that we were assigned (can be accessed on my individual journal page, [[Emmatyrnauer Week 12]]. We divided up what portions we would be responsible for and have planned to meet up before class tomorrow to practice. The paper we were assigned is: Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. The powerpoint presentation and updated excel file can be accessed above under "File Roundup."
#'''What worked well:''' It was very helpful to meet up in person with Katie to begin working on the powerpoint before separating everything out.
#'''What didn't worked well:''' This week I had so much to do including fixing both week 8 and week 10 individual pages and redoing stem because of the mistake I made in excel. I could have asked for an extension on the excel files to allow for more time to work on the presentation. I could have also been in better communication with Blair and Zach this week.
#'''What will we do to fix what didn't work?''' I will communicate more with the professors. Sitting down together with my group will also help to get us all on the same page for the future weeks.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:03, 20 November 2017 (PST)

====Blair - Coder====
As mentioned on my electronic notebook, [[Bhamilton18 Week 12]], this week's assignment Zachary Van Ysseldyk and I worked on the Coder Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project. Zach and I met in person to collaborate on formatting of the team page, individual journal pages and project progress.
#'''What worked well:''' Zach and I worked on better time management as well as expectations for the assignment. We were able to communicate without any hiccups, and meeting up in person was ideal for clarifying issues.
#'''What didn't worked well:''' We were unsure of our progress in the project as our understanding of milestone 4 meant we needed to wait this week on others.
#'''What will we do to fix what didn't work?''' Checking in with our project teams/coders will help us understand how they are doing, as well as how our own progression is lining up.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 19:15, 20 November 2017 (PST)
====Zach - Coder====
This week, Blair and I worked on the coder milestones. We will work on integrating the actual other team's parts as they start to finish. We also collaborated with Emma and Katie to make sure that we were on the same page. 
[[Zvanysse Week 12]] 
#'''Things that went well:''' we were better about our time management as well as we communicated well. We met up together periodically to make sure that we were on the same page.
#'''Things that didn't go well:''' We were a little confused on how to go about the project for our milestone considering that it was more of a waiting game this week rather than actual integration. So, we didn't really know how to quantify our progress.
#'''What we will do to fix it:''' We maybe should have collaborated with the other teams a little bit more to be able and gauge how their projects are coming along.

===Week 14===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I worked on completing the week 10 analysis and visualized a gene regulatory network for the wild type strain with GRNsight. All of the steps I took and files used can be found on my individual page: [[Emmatyrnauer Week 14]].
#'''Things that went well:''' It was nice that I had already completed the week 8 and week 10 corrections so that I could just focus on completing the data analysis. I went in to talk to Dr. Dahlquist with issues that I was having during analysis of the microarray data. This allowed for faster and accurate completion of the analysis. I was also able to contact the data analysis guild with any questions that I had.
#'''Things that didn't go well:''' Everything went pretty smoothly this week; it was very helpful having work time in class to complete my last milestone.
#'''What we will do to fix it:''' For next week, I will continue to work with the data analyst guild to complete final individual tasks for the project. I will also be collaborating more with my group members to pull together the final deliverables, paper, and presentation.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:31, 4 December 2017 (PST)

====Blair - Coder====
This week Zach and I worked on the first integration of the website and added a right click feature to each gene. We met in person and text messaged each other. As mentioned in my electronic notebook, [[Bhamilton18 Week 14]], we found online resources to add this right click feature as well as collaborate with Dr. Dionisio for syntax problems. This week Emma focused on progressing with data analysis for the gene wild type and then Katie made sure all groups were giving us their deliverables.
#'''Things that went well:''' Collaboration with other groups was productive and went smoothly. Having Dr. Dionisio as a resource has been very helpful and quickened the process.
#'''Things that didn't go well:''' Working in D3 syntax has been difficult to progress in certain deliverables.
#'''What we will do to fix it:''' In order to fix this problem, Zach and I hope to work closely with Dr. Dionisio finding external resources and fixing small errors.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 21:25, 4 December 2017 (PST)
====Zach - Coder====
This week Blair and I worked on the first integration by merging through github as well as working on the right click function. This function enabled us to right click and automatically link the gene that was clicked on to that particular gene page. We connected by texting as well as meeting up in person before committing our week's work to make sure that we were on the same page. We mentioned this on my electronic notebook, [[Zvanysse Week 14]]. We collaborated with Dr. Dionisio to work out some of the D3 technical syntax problems that came about. Emma worked on progressing on the data analysis for the gene wild type and Katie make sure that everyone was on task.
#'''What went well:''' Our communication and procrastination was overall much better. Collaborating with other teams went smoothly and connecting with Dr. Dionisio for syntax went well as the problem was diagnosed soon after it became about.
#'''What Didn't go well:''' Working with D3 was a little difficult because the syntax ultimately changed for the API. This was unforeseen so it was a little frustrating.
#'''How will we fix this:''' When it comes to syntax problems, we will be more in communication with Dr. Dionisio 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 21:36, 4 December 2017 (PST)



==Bibliography==
===Paper 1===
Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. ''Cryobiology'', 46(3), 230-237.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212
* PubMed Central: not available
* Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
* Publisher Full Text (PDF): https://electra.lmu.edu:3555/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=4c9b7cc0-c775-11e7-af71-00000aab0f26&acdnat=1510469407_3e02bee4266fd6a211ea3f6e27b460cf
* Copyright: 2003 by Science Direct; article is not Open Access
* Publisher: Elsevier Science
* Availability: online at www.sciencedirect.com
* Did LMU pay a fee for this article: yes

===Paper 2===
Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. ''Extremophiles'', 10(2), 117-128.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome-wide+expression+analysis+of+yeast+response+during+exposure+to+4+degrees+C
* PubMed Central: not available
* Publisher Full Text (HTML): https://electra.lmu.edu:2529/article/10.1007/s00792-005-0480-1
* Publisher Full Text (PDF): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=16254683
* Copyright: 2005 by Springer-Verlag; article is not Open Access
* Publisher: Springer-Verlag
* Availability: online
* Did LMU pay a fee for this article: yes

===Paper 3===
Becerra, M., Lombardia, L. J., González‐Siso, M. I., Rodríguez‐Belmonte, E., Hauser, N. C., & Cerdán, M. E. (2003). Genome‐wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and functional genomics, 4(4), 366-375.

'''PubMed Abstract:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/

'''PubMed Central:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf

'''Publisher Full Text (HTML):''' unavailable

'''Publisher Full Text (PDF):''' http://downloads.hindawi.com/journals/ijg/2003/175356.pdf

'''Copyright:''' Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

'''Publisher:''' Hindawi Publishing Corporation

'''Availability:''' Open access

'''Did LMU pay a fee for this article:''' no

===Paper 4===
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.

'''PubMed Abstract: ''' https://www.ncbi.nlm.nih.gov/pubmed/?term=Comprehensive+expression+analysis+of+time-dependent+genetic+responses+in+yeast+cells+to+low+temperature

'''PubMed Central: ''' not available

'''Publisher Full Text (HTML): ''' http://www.jbc.org/content/277/51/50015.long

'''Publisher Full Text (PDF): ''' http://www.jbc.org/content/277/51/50015.full.pdf

'''Copyright: ''' "Other parties are welcome to copy, distribute, transmit and adapt the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above." from http://www.jbc.org/site/misc/Copyright_Permission.xhtml

'''Publisher: ''' American Society for Biochemistry and Molecular Biology

'''Availability: '''All articles from this journal are free 1 year after publishing.

'''Did LMU pay a fee for this article:''' No.

==Acknowledgments==
#Our group collaborates on this page each week filling out our respective team journal assignments and project updates.
#*WE have a group chat to communicate problems, questions and ideas for our weekly assignments/milestones.
#We utilized the Calendar outline from the [[JASPAR the Friendly Ghost]] page, but changed the milestone/tasks due.

==References==
*Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup- saved-healthcare-gov-the-worst-website-in-america/397784/
*Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf

{{template:Pugs Not Drugs}}

{{GRNsight Gene Page Project Links}}

Bhamilton18 Week 15

2017-12-11T20:58:44Z

Bhamilton18: added wiki signature to acknowledgments

==Notebook for Week 15==
#This week Zach and I focused on major integration of the JASPAR, Gene Database APIs and Page Design teams.
#Due to some communication issues of Week 14, Zach and I were backtracked on certain integrations with other groups, but quickly made up for lost time.
#Our task for week was to add IDs from: NCBI, SGD, Ensembl, Uniprot and JASPAR to the top of the gene page.
#By communicating with Dr. Dionisio we found the correct ID format to reference the info.html file as well as the api.js file.
#*The api.js file contains the data and info.html contains the page layout.
#Each ID was created and required a few git pull commands as the other teams needed to fix api calls and retrieve the correct data.
#Once this was completed, Zach and I worked with the page design team to find places for the data found throughout the api teams api.js file.
#

==Acknowledgments==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the id syntax and class referencing portions.
#Interaction and Integration team worked with JASPAR, Gene Database APIs and Page Design teams throughout integrations.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 12:58, 11 December 2017 (PST)

==References==

LMU BioDB 2017. (2017). Deliverables. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

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

{{Bhamilton18}}

Bhamilton18 Week 15

2017-12-11T05:22:50Z

Bhamilton18: Created notebook and added references, acknowledgments and notebook notes

==Notebook for Week 15==
#This week Zach and I focused on major integration of the JASPAR, Gene Database APIs and Page Design teams.
#Due to some communication issues of Week 14, Zach and I were backtracked on certain integrations with other groups, but quickly made up for lost time.
#Our task for week was to add IDs from: NCBI, SGD, Ensembl, Uniprot and JASPAR to the top of the gene page.
#By communicating with Dr. Dionisio we found the correct ID format to reference the info.html file as well as the api.js file.
#*The api.js file contains the data and info.html contains the page layout.
#Each ID was created and required a few git pull commands as the other teams needed to fix api calls and retrieve the correct data.
#Once this was completed, Zach and I worked with the page design team to find places for the data found throughout the api teams api.js file.
#

==Acknowledgments==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the id syntax and class referencing portions.
#Interaction and Integration team worked with JASPAR, Gene Database APIs and Page Design teams throughout integrations.
#'''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). Deliverables. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

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

{{Bhamilton18}}

Lights, Camera, InterACTION!

2017-12-11T04:16:15Z

Bhamilton18: updated calendar

[[File:PugNotDrugsLogo.png|400px|thumb|right|Pugs Not Drugs Logo]]

==Team Members==
*[[user:bhamilton18|Blair Hamilton]] '''-Coder'''
*[[user:emmatyrnauer|Emma Tyrnauer]] '''-Data Analyst'''
*[[user:kwrigh35|Katie Wright]] '''-Project Manager/Quality Assurance'''
*[[user:zvanysse|Zach Van Ysseldyke]] '''-Coder'''

==File Roundup==
*Week 11 presentation by Blair and Zach: [[media:The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf|The Secret Startup that Saved the Worst Website in America]]
*Week 12 presentation by Emma and Katie: [[media:Genome-wide expression analysis of yeast response during exposure to 4 degrees C.pdf|Genome-wide expression analysis of yeast response during exposure to 4 degrees C]]
*Microarray data excel spreadsheet (corrected) : [[Media:Wt_Microarraydata_ET.zip]]
[[Lights, Camera, InterACTION! Deliverables]]

==Team Schedule== 
{| 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''' <s> C: PPT Presentation PM/DA: Journal Articles</s>
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' <s>C: Complete setup steps (Milestones 0-4) PM/DA: Journal Club Presentations DA: Week 8 and Week 10 edits</s>
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' <s>C: First Integration projected completion</s> <s>PM: Check in with team DA: </s>
|'''29'''
|'''30''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA:</s>
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' <s>C: Check in with groups, and further integrate as needed.</s> PM: Check in with team <s>DA: complete week 10 data analysis</s>
|'''6'''
|'''7''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA: </s>
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==
===Week 11===
====Katie - PM/QA====
For this week, I worked with [[user:emmatyrnauer|Emma]] to find papers to use as reference in our final research paper. Emma and I both found papers that are related to yeast cold shock reactions and most of them use microarray data. I am excited to read these articles more in depth as we develop our research project and paper. Further information can be found on my [[kwrigh35 Week 11|Week 11]] journal page.
#'''What worked?''' Using the three different sources was really helpful because I had never used "Web of Science" before. It was good to learn about how different these results can be, especially with tweaking the search terms a little bit.
#'''What didn't work?''' I had poor time management this week. I waited until Monday to do the majority of the work and definitely should not have done so. The rest of the project went well, however.
#'''What will I do next to fix what didn't work?''' I will plan to meet up with Emma early on in the week so we can work together on our presentation. This way I will be held accountable to get my work done earlier.

====Emma - Data Analysis====
This week Katie and I worked on the annotated bibliography (below). We chose papers that provided more information on yeast gene regulation in response to cold shock. Pub Med, Google Scholar, and Web of Science were utilized to perform basic searches using key words as well as advanced searches which helped to narrow the results. More detailed information can be found on my individual journal entry page: [[Emmatyrnauer Week 11]]. Meanwhile, Blair and Zach worked on coder journal club presentation. Construction of the group page was completed during class.
# Overall, this week went pretty smoothly; Katie and I communicated over text to determine which papers we were going to write the bibliographies for and were available to each other for any questions we had.
# There wasn't really anything that didn't work.
# Since we will be working this next week on our journal club presentation, it might be beneficial to meet in person.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:26, 13 November 2017 (PST)

====Blair - Coder====
This week Zach and I created the Powerpoint presentation about ''The secret startup that saved the worst website in America'' article. We created individual outlines of the article on our respective pages, mine is as follows: [[Bhamilton18 Week 11]]. Our presentation is linked here: [[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]
#Overall, our communication and diving up of tasks went well and smoothly. Meanwhile, Katie and Emma worked on the annotate bibliography. While I primarily worked with Zach our communication amongst group members went well and we hope to continue to do so for the future.
#Something that didn't work as well was our time management. Next time we hope to have more class time and start working earlier on our portion of the assignment.
#For the future, we will continue to communicate in person and through messaging and will work on time management by starting earlier.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 23:35, 13 November 2017 (PST)

====Zach - Coder====
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]] 
[[Zvanysse Week 11]] 
This week, Blair and I created a Powerpoint about the "Secret Startup that saved the worst website in America." We read through the article and picked out the relevant themes and main messages to put on the PowerPoint. We wrote these themes and summaries out on our individual Journals. Then, we collaborated and made our PowerPoint.
#'''Things that went well:''' Blair and I's communication was very strong and we knew exactly what was going on with one another. We knew when we were going to meet up and what was expected for each of us.
#'''Things that didn't go well:''' Blair and I missed the mark on our time management. We did not expect this assignment to take this long. Next time, we will make sure to start on assignments earlier.
#Like I said above, we will plan out exact times earlier on in the week that we can meet up
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 23:44, 13 November 2017 (PST) 

===Week 12===
====Katie - PM/QA====
Emma and I worked on our presentation on "Genome-wide expression analysis of yeast response during exposure to 4 degrees C," details of which can be found on my [[kwrigh35 Week 12|Week 12]] page. The presentation can be found in the "file roundup" section of this page.
#'''What worked?'''Emma and I met up outside of class to work on the assignment, which was really helpful.
#'''What didn't work?'''I underestimated to the time it would take to find 10 terms that I didn't know before reading the paper. It was hard to find 10, so I resorted to picking terms that I knew but wanted to know more about. It was also difficult to find definitions for some of these words, because some of them weren't in biological dictionaries.
#'''What will I do next to fix what didn't work?'''I should start work on the assignment before the weekend begins. That way, I don't have to spend the majority of my Monday afternoon/evening on the project. It is better to be able to come back to a project several times, and each time have "fresh" eyes.

====Emma - Data Analysis====
This week I made all the corrections listed on the talk page of my user page for both [[Emmatyrnauer Week 8]] and [[Emmatyrnauer Week 10]]. This included corrections to the excel files, stem analysis, electronic notebooks, analysis of log fold changes and p values, and the acknowledgements section. Following the completion of fixing the errors in the excel file, I emailed Dr. Dahlquist to ascertain that I completed the analysis correctly. For the individual assignment this week, Katie and I met up to work on our journal club presentation of the paper that we were assigned (can be accessed on my individual journal page, [[Emmatyrnauer Week 12]]. We divided up what portions we would be responsible for and have planned to meet up before class tomorrow to practice. The paper we were assigned is: Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. The powerpoint presentation and updated excel file can be accessed above under "File Roundup."
#'''What worked well:''' It was very helpful to meet up in person with Katie to begin working on the powerpoint before separating everything out.
#'''What didn't worked well:''' This week I had so much to do including fixing both week 8 and week 10 individual pages and redoing stem because of the mistake I made in excel. I could have asked for an extension on the excel files to allow for more time to work on the presentation. I could have also been in better communication with Blair and Zach this week.
#'''What will we do to fix what didn't work?''' I will communicate more with the professors. Sitting down together with my group will also help to get us all on the same page for the future weeks.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:03, 20 November 2017 (PST)

====Blair - Coder====
As mentioned on my electronic notebook, [[Bhamilton18 Week 12]], this week's assignment Zachary Van Ysseldyk and I worked on the Coder Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project. Zach and I met in person to collaborate on formatting of the team page, individual journal pages and project progress.
#'''What worked well:''' Zach and I worked on better time management as well as expectations for the assignment. We were able to communicate without any hiccups, and meeting up in person was ideal for clarifying issues.
#'''What didn't worked well:''' We were unsure of our progress in the project as our understanding of milestone 4 meant we needed to wait this week on others.
#'''What will we do to fix what didn't work?''' Checking in with our project teams/coders will help us understand how they are doing, as well as how our own progression is lining up.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 19:15, 20 November 2017 (PST)
====Zach - Coder====
This week, Blair and I worked on the coder milestones. We will work on integrating the actual other team's parts as they start to finish. We also collaborated with Emma and Katie to make sure that we were on the same page. 
[[Zvanysse Week 12]] 
#'''Things that went well:''' we were better about our time management as well as we communicated well. We met up together periodically to make sure that we were on the same page.
#'''Things that didn't go well:''' We were a little confused on how to go about the project for our milestone considering that it was more of a waiting game this week rather than actual integration. So, we didn't really know how to quantify our progress.
#'''What we will do to fix it:''' We maybe should have collaborated with the other teams a little bit more to be able and gauge how their projects are coming along.

===Week 14===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I worked on completing the week 10 analysis and visualized a gene regulatory network for the wild type strain with GRNsight. All of the steps I took and files used can be found on my individual page: [[Emmatyrnauer Week 14]].
#'''Things that went well:''' It was nice that I had already completed the week 8 and week 10 corrections so that I could just focus on completing the data analysis. I went in to talk to Dr. Dahlquist with issues that I was having during analysis of the microarray data. This allowed for faster and accurate completion of the analysis. I was also able to contact the data analysis guild with any questions that I had.
#'''Things that didn't go well:''' Everything went pretty smoothly this week; it was very helpful having work time in class to complete my last milestone.
#'''What we will do to fix it:''' For next week, I will continue to work with the data analyst guild to complete final individual tasks for the project. I will also be collaborating more with my group members to pull together the final deliverables, paper, and presentation.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:31, 4 December 2017 (PST)

====Blair - Coder====
This week Zach and I worked on the first integration of the website and added a right click feature to each gene. We met in person and text messaged each other. As mentioned in my electronic notebook, [[Bhamilton18 Week 14]], we found online resources to add this right click feature as well as collaborate with Dr. Dionisio for syntax problems. This week Emma focused on progressing with data analysis for the gene wild type and then Katie made sure all groups were giving us their deliverables.
#'''Things that went well:''' Collaboration with other groups was productive and went smoothly. Having Dr. Dionisio as a resource has been very helpful and quickened the process.
#'''Things that didn't go well:''' Working in D3 syntax has been difficult to progress in certain deliverables.
#'''What we will do to fix it:''' In order to fix this problem, Zach and I hope to work closely with Dr. Dionisio finding external resources and fixing small errors.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 21:25, 4 December 2017 (PST)
====Zach - Coder====
This week Blair and I worked on the first integration by merging through github as well as working on the right click function. This function enabled us to right click and automatically link the gene that was clicked on to that particular gene page. We connected by texting as well as meeting up in person before committing our week's work to make sure that we were on the same page. We mentioned this on my electronic notebook, [[Zvanysse Week 14]]. We collaborated with Dr. Dionisio to work out some of the D3 technical syntax problems that came about. Emma worked on progressing on the data analysis for the gene wild type and Katie make sure that everyone was on task.
#'''What went well:''' Our communication and procrastination was overall much better. Collaborating with other teams went smoothly and connecting with Dr. Dionisio for syntax went well as the problem was diagnosed soon after it became about.
#'''What Didn't go well:''' Working with D3 was a little difficult because the syntax ultimately changed for the API. This was unforeseen so it was a little frustrating.
#'''How will we fix this:''' When it comes to syntax problems, we will be more in communication with Dr. Dionisio 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 21:36, 4 December 2017 (PST)



==Bibliography==
===Paper 1===
Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. ''Cryobiology'', 46(3), 230-237.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212
* PubMed Central: not available
* Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
* Publisher Full Text (PDF): https://electra.lmu.edu:3555/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=4c9b7cc0-c775-11e7-af71-00000aab0f26&acdnat=1510469407_3e02bee4266fd6a211ea3f6e27b460cf
* Copyright: 2003 by Science Direct; article is not Open Access
* Publisher: Elsevier Science
* Availability: online at www.sciencedirect.com
* Did LMU pay a fee for this article: yes

===Paper 2===
Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. ''Extremophiles'', 10(2), 117-128.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome-wide+expression+analysis+of+yeast+response+during+exposure+to+4+degrees+C
* PubMed Central: not available
* Publisher Full Text (HTML): https://electra.lmu.edu:2529/article/10.1007/s00792-005-0480-1
* Publisher Full Text (PDF): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=16254683
* Copyright: 2005 by Springer-Verlag; article is not Open Access
* Publisher: Springer-Verlag
* Availability: online
* Did LMU pay a fee for this article: yes

===Paper 3===
Becerra, M., Lombardia, L. J., González‐Siso, M. I., Rodríguez‐Belmonte, E., Hauser, N. C., & Cerdán, M. E. (2003). Genome‐wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and functional genomics, 4(4), 366-375.

'''PubMed Abstract:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/

'''PubMed Central:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf

'''Publisher Full Text (HTML):''' unavailable

'''Publisher Full Text (PDF):''' http://downloads.hindawi.com/journals/ijg/2003/175356.pdf

'''Copyright:''' Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

'''Publisher:''' Hindawi Publishing Corporation

'''Availability:''' Open access

'''Did LMU pay a fee for this article:''' no

===Paper 4===
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.

'''PubMed Abstract: ''' https://www.ncbi.nlm.nih.gov/pubmed/?term=Comprehensive+expression+analysis+of+time-dependent+genetic+responses+in+yeast+cells+to+low+temperature

'''PubMed Central: ''' not available

'''Publisher Full Text (HTML): ''' http://www.jbc.org/content/277/51/50015.long

'''Publisher Full Text (PDF): ''' http://www.jbc.org/content/277/51/50015.full.pdf

'''Copyright: ''' "Other parties are welcome to copy, distribute, transmit and adapt the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above." from http://www.jbc.org/site/misc/Copyright_Permission.xhtml

'''Publisher: ''' American Society for Biochemistry and Molecular Biology

'''Availability: '''All articles from this journal are free 1 year after publishing.

'''Did LMU pay a fee for this article:''' No.

==Acknowledgments==
#Our group collaborates on this page each week filling out our respective team journal assignments and project updates.
#*WE have a group chat to communicate problems, questions and ideas for our weekly assignments/milestones.
#We utilized the Calendar outline from the [[JASPAR the Friendly Ghost]] page, but changed the milestone/tasks due.

==References==
*Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup- saved-healthcare-gov-the-worst-website-in-america/397784/
*Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf

{{template:Pugs Not Drugs}}

{{GRNsight Gene Page Project Links}}

Bhamilton18 Week 14

2017-12-05T05:28:57Z

Bhamilton18: added to notebook

==Electronic Lab Notebook==
This week [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked to progress the Coder portion of our Interaction and Integration section of the final project.
#To begin we had a group meeting in order to gauge the progress of each member in the group.
#Zach and I also met with Dondi in order to work on syntax for our coding part of the assignment.
#We began by trying to have the user '''right''' click on any of the genes of the GRNsight page to open any page.
#*For our purposes we used this weskit to link to the page: http://dogtime.com/dog-breeds/pug#/slide/1
#*It is important to note we did not care which website we were going to, we just wanted to link the right click to some website.
#Next, we worked on creating a simple web page, similar to our gene pages, in which the site can link to instead of the outside website source.
#*One problem we realized was happening was that Safari and Chrome believe the websites are pop-ups and therefore blocks them.
#*We have not fixed this problem yet but we have noted it.
# href: "/gene/info.html?" + $.param({symbol: gene.name}),
#* This code allows the right click to go to a generic page called info.html
#*Next the parameters goes to the gene selected and gives it's name.
#**I.e if "HOT1" is right clicked the new page will show a console.log of the gene name.
#Finally we merged the other groups work for the first integration. All went smoothly and we will be collaborating more with groups soon.
#*This merge was done through GitHub and pushed to our GitHub branch: https://github.com/bhamilton18/GRNsight

==Acknowledgements==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the D3 syntax and working through the right click problem.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

==References==
#Get url parameter jquery Or How to Get Query String Values In js. Retrieved December 04, 2017, from https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js
#How to retrieve GET parameters from javascript? Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
#JavaScript Window Location. Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
#LMU BioDB 2017. (2017). Coder. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Coder
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
#Window.location. Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Bhamilton18}}

Lights, Camera, InterACTION!

2017-12-05T05:25:55Z

Bhamilton18: Added summary and journal entry

[[File:PugNotDrugsLogo.png|400px|thumb|right|Pugs Not Drugs Logo]]

==Team Members==
*[[user:bhamilton18|Blair Hamilton]] '''-Coder'''
*[[user:emmatyrnauer|Emma Tyrnauer]] '''-Data Analyst'''
*[[user:kwrigh35|Katie Wright]] '''-Project Manager/Quality Assurance'''
*[[user:zvanysse|Zach Van Ysseldyke]] '''-Coder'''

==File Roundup==
*Week 11 presentation by Blair and Zach: [[media:The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf|The Secret Startup that Saved the Worst Website in America]]
*Week 12 presentation by Emma and Katie: [[media:Genome-wide expression analysis of yeast response during exposure to 4 degrees C.pdf|Genome-wide expression analysis of yeast response during exposure to 4 degrees C]]
*Microarray data excel spreadsheet (corrected) : [[Media:Wt_Microarraydata_ET.zip]]

==Team Schedule== 
{| 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''' <s> C: PPT Presentation PM/DA: Journal Articles</s>
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' <s>C: Complete setup steps (Milestones 0-4) PM/DA: Journal Club Presentations DA: Week 8 and Week 10 edits</s>
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' <s>C: First Integration projected completion</s> PM: Check in with team DA:
|'''29'''
|'''30''' C: Check in with other groups about progress PM: Check in with team DA:
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Check in with groups, and further integrate as needed. PM: Check in with team <s>DA: complete week 10 data analysis</s>
|'''6'''
|'''7''' C: Check in with other groups about progress PM: Check in with team DA:
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==
===Week 11===
====Katie - PM/QA====
For this week, I worked with [[user:emmatyrnauer|Emma]] to find papers to use as reference in our final research paper. Emma and I both found papers that are related to yeast cold shock reactions and most of them use microarray data. I am excited to read these articles more in depth as we develop our research project and paper. Further information can be found on my [[kwrigh35 Week 11|Week 11]] journal page.
#'''What worked?''' Using the three different sources was really helpful because I had never used "Web of Science" before. It was good to learn about how different these results can be, especially with tweaking the search terms a little bit.
#'''What didn't work?''' I had poor time management this week. I waited until Monday to do the majority of the work and definitely should not have done so. The rest of the project went well, however.
#'''What will I do next to fix what didn't work?''' I will plan to meet up with Emma early on in the week so we can work together on our presentation. This way I will be held accountable to get my work done earlier.

====Emma - Data Analysis====
This week Katie and I worked on the annotated bibliography (below). We chose papers that provided more information on yeast gene regulation in response to cold shock. Pub Med, Google Scholar, and Web of Science were utilized to perform basic searches using key words as well as advanced searches which helped to narrow the results. More detailed information can be found on my individual journal entry page: [[Emmatyrnauer Week 11]]. Meanwhile, Blair and Zach worked on coder journal club presentation. Construction of the group page was completed during class.
# Overall, this week went pretty smoothly; Katie and I communicated over text to determine which papers we were going to write the bibliographies for and were available to each other for any questions we had.
# There wasn't really anything that didn't work.
# Since we will be working this next week on our journal club presentation, it might be beneficial to meet in person.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:26, 13 November 2017 (PST)

====Blair - Coder====
This week Zach and I created the Powerpoint presentation about ''The secret startup that saved the worst website in America'' article. We created individual outlines of the article on our respective pages, mine is as follows: [[Bhamilton18 Week 11]]. Our presentation is linked here: [[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]
#Overall, our communication and diving up of tasks went well and smoothly. Meanwhile, Katie and Emma worked on the annotate bibliography. While I primarily worked with Zach our communication amongst group members went well and we hope to continue to do so for the future.
#Something that didn't work as well was our time management. Next time we hope to have more class time and start working earlier on our portion of the assignment.
#For the future, we will continue to communicate in person and through messaging and will work on time management by starting earlier.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 23:35, 13 November 2017 (PST)

====Zach - Coder====
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]] 
[[Zvanysse Week 11]] 
This week, Blair and I created a Powerpoint about the "Secret Startup that saved the worst website in America." We read through the article and picked out the relevant themes and main messages to put on the PowerPoint. We wrote these themes and summaries out on our individual Journals. Then, we collaborated and made our PowerPoint.
#'''Things that went well:''' Blair and I's communication was very strong and we knew exactly what was going on with one another. We knew when we were going to meet up and what was expected for each of us.
#'''Things that didn't go well:''' Blair and I missed the mark on our time management. We did not expect this assignment to take this long. Next time, we will make sure to start on assignments earlier.
#Like I said above, we will plan out exact times earlier on in the week that we can meet up
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 23:44, 13 November 2017 (PST) 

===Week 12===
====Katie - PM/QA====
Emma and I worked on our presentation on "Genome-wide expression analysis of yeast response during exposure to 4 degrees C," details of which can be found on my [[kwrigh35 Week 12|Week 12]] page. The presentation can be found in the "file roundup" section of this page.
#'''What worked?'''Emma and I met up outside of class to work on the assignment, which was really helpful.
#'''What didn't work?'''I underestimated to the time it would take to find 10 terms that I didn't know before reading the paper. It was hard to find 10, so I resorted to picking terms that I knew but wanted to know more about. It was also difficult to find definitions for some of these words, because some of them weren't in biological dictionaries.
#'''What will I do next to fix what didn't work?'''I should start work on the assignment before the weekend begins. That way, I don't have to spend the majority of my Monday afternoon/evening on the project. It is better to be able to come back to a project several times, and each time have "fresh" eyes.

====Emma - Data Analysis====
This week I made all the corrections listed on the talk page of my user page for both [[Emmatyrnauer Week 8]] and [[Emmatyrnauer Week 10]]. This included corrections to the excel files, stem analysis, electronic notebooks, analysis of log fold changes and p values, and the acknowledgements section. Following the completion of fixing the errors in the excel file, I emailed Dr. Dahlquist to ascertain that I completed the analysis correctly. For the individual assignment this week, Katie and I met up to work on our journal club presentation of the paper that we were assigned (can be accessed on my individual journal page, [[Emmatyrnauer Week 12]]. We divided up what portions we would be responsible for and have planned to meet up before class tomorrow to practice. The paper we were assigned is: Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. The powerpoint presentation and updated excel file can be accessed above under "File Roundup."
#'''What worked well:''' It was very helpful to meet up in person with Katie to begin working on the powerpoint before separating everything out.
#'''What didn't worked well:''' This week I had so much to do including fixing both week 8 and week 10 individual pages and redoing stem because of the mistake I made in excel. I could have asked for an extension on the excel files to allow for more time to work on the presentation. I could have also been in better communication with Blair and Zach this week.
#'''What will we do to fix what didn't work?''' I will communicate more with the professors. Sitting down together with my group will also help to get us all on the same page for the future weeks.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:03, 20 November 2017 (PST)

====Blair - Coder====
As mentioned on my electronic notebook, [[Bhamilton18 Week 12]], this week's assignment Zachary Van Ysseldyk and I worked on the Coder Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project. Zach and I met in person to collaborate on formatting of the team page, individual journal pages and project progress.
#'''What worked well:''' Zach and I worked on better time management as well as expectations for the assignment. We were able to communicate without any hiccups, and meeting up in person was ideal for clarifying issues.
#'''What didn't worked well:''' We were unsure of our progress in the project as our understanding of milestone 4 meant we needed to wait this week on others.
#'''What will we do to fix what didn't work?''' Checking in with our project teams/coders will help us understand how they are doing, as well as how our own progression is lining up.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 19:15, 20 November 2017 (PST)
====Zach - Coder====
This week, Blair and I worked on the coder milestones. We will work on integrating the actual other team's parts as they start to finish. We also collaborated with Emma and Katie to make sure that we were on the same page. 
[[Zvanysse Week 12]] 
#'''Things that went well:''' we were better about our time management as well as we communicated well. We met up together periodically to make sure that we were on the same page.
#'''Things that didn't go well:''' We were a little confused on how to go about the project for our milestone considering that it was more of a waiting game this week rather than actual integration. So, we didn't really know how to quantify our progress.
#'''What we will do to fix it:''' We maybe should have collaborated with the other teams a little bit more to be able and gauge how their projects are coming along.

===Week 14===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I worked on completing the week 10 analysis and visualized a gene regulatory network for the wild type strain with GRNsight. All of the steps I took and files used can be found on my individual page: [[Emmatyrnauer Week 14]].
#'''Things that went well:''' It was nice that I had already completed the week 8 and week 10 corrections so that I could just focus on completing the data analysis. I went in to talk to Dr. Dahlquist with issues that I was having during analysis of the microarray data. This allowed for faster and accurate completion of the analysis. I was also able to contact the data analysis guild with any questions that I had.
#'''Things that didn't go well:''' Everything went pretty smoothly this week; it was very helpful having work time in class to complete my last milestone.
#'''What we will do to fix it:''' For next week, I will continue to work with the data analyst guild to complete final individual tasks for the project. I will also be collaborating more with my group members to pull together the final deliverables, paper, and presentation.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:31, 4 December 2017 (PST)

====Blair - Coder====
This week Zach and I worked on the first integration of the website and added a right click feature to each gene. We met in person and text messaged each other. As mentioned in my electronic notebook, [[Bhamilton18 Week 14]], we found online resources to add this right click feature as well as collaborate with Dr. Dionisio for syntax problems. This week Emma focused on progressing with data analysis for the gene wild type and then Katie made sure all groups were giving us their deliverables.
#'''Things that went well:''' Collaboration with other groups was productive and went smoothly. Having Dr. Dionisio as a resource has been very helpful and quickened the process.
#'''Things that didn't go well:''' Working in D3 syntax has been difficult to progress in certain deliverables.
#'''What we will do to fix it:''' In order to fix this problem, Zach and I hope to work closely with Dr. Dionisio finding external resources and fixing small errors.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 21:25, 4 December 2017 (PST)
====Zach - Coder====



==Bibliography==
===Paper 1===
Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. ''Cryobiology'', 46(3), 230-237.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212
* PubMed Central: not available
* Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
* Publisher Full Text (PDF): https://electra.lmu.edu:3555/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=4c9b7cc0-c775-11e7-af71-00000aab0f26&acdnat=1510469407_3e02bee4266fd6a211ea3f6e27b460cf
* Copyright: 2003 by Science Direct; article is not Open Access
* Publisher: Elsevier Science
* Availability: online at www.sciencedirect.com
* Did LMU pay a fee for this article: yes

===Paper 2===
Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. ''Extremophiles'', 10(2), 117-128.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome-wide+expression+analysis+of+yeast+response+during+exposure+to+4+degrees+C
* PubMed Central: not available
* Publisher Full Text (HTML): https://electra.lmu.edu:2529/article/10.1007/s00792-005-0480-1
* Publisher Full Text (PDF): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=16254683
* Copyright: 2005 by Springer-Verlag; article is not Open Access
* Publisher: Springer-Verlag
* Availability: online
* Did LMU pay a fee for this article: yes

===Paper 3===
Becerra, M., Lombardia, L. J., González‐Siso, M. I., Rodríguez‐Belmonte, E., Hauser, N. C., & Cerdán, M. E. (2003). Genome‐wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and functional genomics, 4(4), 366-375.

'''PubMed Abstract:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/

'''PubMed Central:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf

'''Publisher Full Text (HTML):''' unavailable

'''Publisher Full Text (PDF):''' http://downloads.hindawi.com/journals/ijg/2003/175356.pdf

'''Copyright:''' Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

'''Publisher:''' Hindawi Publishing Corporation

'''Availability:''' Open access

'''Did LMU pay a fee for this article:''' no

===Paper 4===
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.

'''PubMed Abstract: ''' https://www.ncbi.nlm.nih.gov/pubmed/?term=Comprehensive+expression+analysis+of+time-dependent+genetic+responses+in+yeast+cells+to+low+temperature

'''PubMed Central: ''' not available

'''Publisher Full Text (HTML): ''' http://www.jbc.org/content/277/51/50015.long

'''Publisher Full Text (PDF): ''' http://www.jbc.org/content/277/51/50015.full.pdf

'''Copyright: ''' "Other parties are welcome to copy, distribute, transmit and adapt the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above." from http://www.jbc.org/site/misc/Copyright_Permission.xhtml

'''Publisher: ''' American Society for Biochemistry and Molecular Biology

'''Availability: '''All articles from this journal are free 1 year after publishing.

'''Did LMU pay a fee for this article:''' No.

==Acknowledgments==
#Our group collaborates on this page each week filling out our respective team journal assignments and project updates.
#*WE have a group chat to communicate problems, questions and ideas for our weekly assignments/milestones.
#We utilized the Calendar outline from the [[JASPAR the Friendly Ghost]] page, but changed the milestone/tasks due.

==References==
*Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup- saved-healthcare-gov-the-worst-website-in-america/397784/
*Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf

{{template:Pugs Not Drugs}}

{{GRNsight Gene Page Project Links}}

Bhamilton18 Week 14

2017-12-05T05:13:08Z

Bhamilton18: reformatted

==Electronic Lab Notebook==
This week [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked to progress the Coder portion of our Interaction and Integration section of the final project.
#To begin we had a group meeting in order to gauge the progress of each member in the group.
#Zach and I also met with Dondi in order to work on syntax for our coding part of the assignment.
#We began by trying to have the user '''right''' click on any of the genes of the GRNsight page to open any page.
#*For our purposes we used this weskit to link to the page: http://dogtime.com/dog-breeds/pug#/slide/1
#*It is important to note we did not care which website we were going to, we just wanted to link the right click to some website.
#Next, we worked on creating a simple web page, similar to our gene pages, in which the site can link to instead of the outside website source.
#*One problem we realized was happening was that Safari and Chrome believe the websites are pop-ups and therefore blocks them.
#*We have not fixed this problem yet but we have noted it.
# href: "/gene/info.html?" + $.param({symbol: gene.name}),
#* This code allows the right click to go to a generic page called info.html
#*Next the parameters goes to the gene selected and gives it's name.
#**I.e if "HOT1" is right clicked the new page will show a console.log of the gene name.
#Finally we merged the other groups work for the first integration. All went smoothly and we will be collaborating more with groups soon.

==Acknowledgements==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the D3 syntax and working through the right click problem.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

==References==
#Get url parameter jquery Or How to Get Query String Values In js. Retrieved December 04, 2017, from https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js
#How to retrieve GET parameters from javascript? Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
#JavaScript Window Location. Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
#LMU BioDB 2017. (2017). Coder. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Coder
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
#Window.location. Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Bhamilton18}}

Bhamilton18 Week 14

2017-12-05T05:05:27Z

Bhamilton18: added to acknowledgments

==Electronic Lab Notebook==
This week [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked to progress the Coder portion of our Interaction and Integration section of the final project.
#To begin we had a group meeting in order to gauge the progress of each member in the group.
#Zach and I also met with Dondi in order to work on syntax for our coding part of the assignment.
#We began by trying to have the user '''right''' click on any of the genes of the GRNsight page to open any page.
#*For our purposes we used this weskit to link to the page: http://dogtime.com/dog-breeds/pug#/slide/1
#*It is important to note we did not care which website we were going to, we just wanted to link the right click to some website.
#Next, we worked on creating a simple web page, similar to our gene pages, in which the site can link to instead of the outside website source.
#*One problem we realized was happening was that Safari and Chrome believe the websites are pop-ups and therefore blocks them.
#*We have not fixed this problem yet but we have noted it.
# href: "/gene/info.html?" + $.param({symbol: gene.name}),
#* This code allows the right click to go to a generic page called info.html
#*Next the parameters goes to the gene selected and gives it's name.
#**I.e if "HOT1" is right clicked the new page will show a console.log of the gene name.
#Finally we merged the other groups work for the first integration. All went smoothly and we will be collaborating more with groups soon.

==Acknowledgements==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#We collaborated with Dr. Dionisio on the D3 syntax and working through the right click problem.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

==References==
===References===
#Get url parameter jquery Or How to Get Query String Values In js. Retrieved December 04, 2017, from https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js
#How to retrieve GET parameters from javascript? Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
#JavaScript Window Location. Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
#LMU BioDB 2017. (2017). Coder. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Coder
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
#Window.location. Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Bhamilton18}}

Bhamilton18 Week 14

2017-12-05T05:04:26Z

Bhamilton18: Added to notebook

==Electronic Lab Notebook==
This week [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked to progress the Coder portion of our Interaction and Integration section of the final project.
#To begin we had a group meeting in order to gauge the progress of each member in the group.
#Zach and I also met with Dondi in order to work on syntax for our coding part of the assignment.
#We began by trying to have the user '''right''' click on any of the genes of the GRNsight page to open any page.
#*For our purposes we used this weskit to link to the page: http://dogtime.com/dog-breeds/pug#/slide/1
#*It is important to note we did not care which website we were going to, we just wanted to link the right click to some website.
#Next, we worked on creating a simple web page, similar to our gene pages, in which the site can link to instead of the outside website source.
#*One problem we realized was happening was that Safari and Chrome believe the websites are pop-ups and therefore blocks them.
#*We have not fixed this problem yet but we have noted it.
# href: "/gene/info.html?" + $.param({symbol: gene.name}),
#* This code allows the right click to go to a generic page called info.html
#*Next the parameters goes to the gene selected and gives it's name.
#**I.e if "HOT1" is right clicked the new page will show a console.log of the gene name.
#Finally we merged the other groups work for the first integration. All went smoothly and we will be collaborating more with groups soon.

==Acknowledgements==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

==References==
===References===
#Get url parameter jquery Or How to Get Query String Values In js. Retrieved December 04, 2017, from https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js
#How to retrieve GET parameters from javascript? Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
#JavaScript Window Location. Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
#LMU BioDB 2017. (2017). Coder. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Coder
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
#Window.location. Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Bhamilton18}}

Bhamilton18 Week 14

2017-12-05T05:02:55Z

Bhamilton18: Added references

==Electronic Lab Notebook==
This week [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked to progress the Coder portion of our Interaction and Integration section of the final project.
#To begin we had a group meeting in order to gauge the progress of each member in the group.
#Zach and I also met with Dondi in order to work on syntax for our coding part of the assignment.
#We began by trying to have the user '''right''' click on any of the genes of the GRNsight page to open any page.
#*For our purposes we used this weskit to link to the page: http://dogtime.com/dog-breeds/pug#/slide/1
#*It is important to note we did not care which website we were going to, we just wanted to link the right click to some website.
#Next, we worked on creating a simple web page, similar to our gene pages, in which the site can link to instead of the outside website source.
#*One problem we realized was happening was that Safari and Chrome believe the websites are pop-ups and therefore blocks them.
#*We have not fixed this problem yet but we have noted it.
# href: "/gene/info.html?" + $.param({symbol: gene.name}),
#* This code allows the right click to go to a generic page called info.html
#*Next the parameters goes to the gene selected and gives it's name.
#**I.e if "HOT1" is right clicked the new page will show a console.log of the gene name.

==Acknowledgements==
#I worked with [[User:Zvanysse|Zachary Van Ysseldyk]] to collaborate on the integration portion of our assignment. We meet in person as well as messaged each other with questions.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

==References==
===References===
#Get url parameter jquery Or How to Get Query String Values In js. Retrieved December 04, 2017, from https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js
#How to retrieve GET parameters from javascript? Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
#JavaScript Window Location. Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
#LMU BioDB 2017. (2017). Coder. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Coder
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
#Window.location. Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Bhamilton18}}

Bhamilton18 Week 14

2017-12-05T04:57:24Z

Bhamilton18: Added to summary of work in notebook

Bhamilton18 Week 14

2017-12-05T00:44:48Z

Bhamilton18: Created page and added small summary of progress

Template:Pugs Not Drugs

2017-11-21T04:22:08Z

Bhamilton18: github addition

==Navigational Links==

{| class="wikitable" style="Background: honeydew"
|-
!style="background: mediumseagreen;color:white"| Category
!style="background: mediumseagreen;color:white"| Links
|-
|'''Interwiki''' ||style="width:575px"| [[Main Page]] &emsp; [[Main_Page#Course_Schedule|Course schedule]] &emsp; [[Lights, Camera, InterACTION!]]
|-
|'''Team Members''' || [[User:Bhamilton18|Blair Hamilton]] &emsp; [[user:emmatyrnauer|Emma Tyrnauer]] &emsp; [[User:Kwrigh35|Katie Wright]] &emsp; [[user:zvanysse|Zach Van Ysseldyk]]
|-
| '''GRNsight Gene Page''' '''Project Instructions''' ||style="width:500px"| [[GRNsight Gene Page Project | Main Instructions]] &emsp; [[GRNsight Gene Page Project Deliverables | Project Deliverables]] &emsp; [[Week 11]] &emsp; [[Week 12]] &emsp; [[Week 14]] &emsp; [[Week 15]]
|-
|'''Guilds''' || [[Project Manager]] &emsp; [[Quality Assurance]] &emsp; [[Data Analysis]] &emsp; [[Coder]]
|-
|'''GitHub GRNsight Link''' || https://github.com/bhamilton18/GRNsight
|-
|}

[[category:Group Projects]]
[[category:Lights, Camera, InterACTION!]]

Lights, Camera, InterACTION!

2017-11-21T03:22:49Z

Bhamilton18: added communication resources

Lights, Camera, InterACTION!

2017-11-21T03:21:23Z

Bhamilton18: formatting problem

Lights, Camera, InterACTION!

2017-11-21T03:19:57Z

Bhamilton18: added strikeouts

Lights, Camera, InterACTION!

2017-11-21T03:17:15Z

Bhamilton18: formatting

Lights, Camera, InterACTION!

2017-11-21T03:15:10Z

Bhamilton18: added signature

Lights, Camera, InterACTION!

2017-11-21T03:14:26Z

Bhamilton18: Added calendar and acknowledgments

Lights, Camera, InterACTION!

2017-11-21T02:56:40Z

Bhamilton18: Added week 12 summary/journal

Lights, Camera, InterACTION!

2017-11-21T02:47:49Z

Bhamilton18: Added reference to Zach and Blair's paper

Bhamilton18 Week 12

2017-11-21T02:46:30Z

Bhamilton18: fixed typos

==Electronic Notebook==
For this week's assignment [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked on the [[Coder]] Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project.

===Milestone 0===
#This portion of the assignment was completed in the [[Week 11]] journal club presentation. The powerpoint can be found here:
#*[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]

===Milestone 1===
#This portion required our individual computers had the correct software to complete the project.
#The following were already on my computer/downloaded to meet the requirements of this milestone:
#* Node.js 8.4.0
#* Code-savvy editor (Atom for my case)
#* Web browser with developer tools (Chrome for my case)
#* '''git''' version control software
#* '''curl''' command

===Milestone 2===
#This portion required me to '''fork''' the open source [https://github.com/dondi/GRNsight GRNsight project].
#*This is found in the top right corner of the GRNsight GitHub project page.
#I added each coder as a collaborator on the project to allow them to create individual branches for their own project milestones/work.
#The fork is currently under my GitHub account: Bhamilton18.

===Milestone 3===
#For this portion the following steps were needed to download the GRNsight GitHub code:
#* '''git clone''' the GitHub fork created and downloaded to Atom.
#* '''cd''' into the folder that contains the cloned repository
#* '''git checkout''' the branch that is assigned to you:
#** Interaction and Integration: ''master'' was our respective branch.
# We followed the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

===Milestone 4===
#This portion of the assignment was a bit slow due to our collaboration with other groups milestones. Once they complete their respective tasks, we will begin integrating them onto the GRNsight GitHub.
#Instead, Zach and I explored the GRNsight code and worked on our team page based on the week 11 feedback from Dr. Dahlquist.

==Acknowledgments==
#For this week's assignment I collaborated with my group members, [[User:Zvanysse|Zachary Van Ysseldyk]], [[User:kwrigh35|Katie Wright]] and [[User:Emmatyrnauer|Emma Tyrnauer]] to complete individual portions of the final group project. We primarily communicated through text to clarify homework questions and update progress of the project.
#*Zach and I met in person and collaborated on formatting of the notebook page, as well as, discussed milestones.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
==References==
LMU BioDB 2017. (2017). Week 12. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

{{Bhamilton18}}

Bhamilton18 Week 12

2017-11-21T02:45:21Z

Bhamilton18: Milestone 4 added

==Electronic Notebook==
For this week's assignment [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked on the [[Coder]] Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project.

===Milestone 0===
#This portion of the assignment was completed in the [[Week 11]] journal club presentation. The powerpoint can be found here:
#*[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]

===Milestone 1===
#This portion required our individual computers had the correct software to complete the project.
#The following were already on my computer/downloaded to meet the requirements of this milestone:
#* Node.js 8.4.0
#* Code-savvy editor (Atom for my case)
#* Web browser with developer tools (Chrome for my case)
#* '''git''' version control software
#* '''curl''' command

===Milestone 2===
#This portion required me to '''fork''' the open source [https://github.com/dondi/GRNsight GRNsight project].
#*This is found in the top right corner of the GRNsight GitHub project page.
#I added each coder as a collaborator on the project to allow them to create individual branches for their own project milestones/work.
#The fork is currently under my GitHub account: Bhamilton18.

===Milestone 3===
#For this portion the following steps were needed to download the GRNsight GitHub code:
#* '''git clone''' the GitHub fork created and downloaded to Atom.
#* '''cd''' into the folder that contains the cloned repository
#* '''git checkout''' the branch that is assigned to you:
#** Interaction and Integration: ''master'' was our respective branch.
# We followed the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

===Milestone 4===
#This portion of the assignment was a bit slow due to our collaboration with other groups milestones. Once they complete their respective tasks, we will begin integrating them onto the GRNsight GitHub.
#Instead,Zach and I explored the GRNsight code and worked on our team page based on the week 11 feedback from Dr. Dahlquist.

==Acknowledgments==
#For this week's assignment I collaborated with my group members, [[User:Zvanysse|Zachary Van Ysseldyk]], [[User:kwrigh35|Katie Wright]] and [[User:Emmatyrnauer|Emma Tyrnauer]] to complete individual portions of the final group project. We primarily communicated through text to clarify homework questions and update progress of the project.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
==References==
LMU BioDB 2017. (2017). Week 12. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

{{Bhamilton18}}

Bhamilton18 Week 12

2017-11-21T02:34:22Z

Bhamilton18: Added Milestone 3

==Electronic Notebook==
For this week's assignment [[User:Zvanysse|Zachary Van Ysseldyk]] and I worked on the [[Coder]] Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project.

===Milestone 0===
#This portion of the assignment was completed in the [[Week 11]] journal club presentation. The powerpoint can be found here:
#*[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]

===Milestone 1===
#This portion required our individual computers had the correct software to complete the project.
#The following were already on my computer/downloaded to meet the requirements of this milestone:
#* Node.js 8.4.0
#* Code-savvy editor (Atom for my case)
#* Web browser with developer tools (Chrome for my case)
#* '''git''' version control software
#* '''curl''' command

===Milestone 2===
#This portion required me to '''fork''' the open source [https://github.com/dondi/GRNsight GRNsight project].
#*This is found in the top right corner of the GRNsight GitHub project page.
#I added each coder as a collaborator on the project to allow them to create individual branches for their own project milestones/work.
#The fork is currently under my GitHub account: Bhamilton18.

===Milestone 3===
#For this portion the following steps were needed to download the GRNsight GitHub code:
#* '''git clone''' the GitHub fork created and downloaded to Atom.
#* '''cd''' into the folder that contains the cloned repository
#* '''git checkout''' the branch that is assigned to you:
#** Interaction and Integration: ''master'' was our respective branch.
# We followed the [https://github.com/dondi/GRNsight/wiki/Running-the-Applications instructions in the GRNsight wiki] to perform the following:
## Installation of necessary third-party libraries
## Initial startup of the GRNsight application ''on your computer''

===Milestone 4===

==Acknowledgments==
#For this week's assignment I collaborated with my group members, [[User:Zvanysse|Zachary Van Ysseldyk]], [[User:kwrigh35|Katie Wright]] and [[User:Emmatyrnauer|Emma Tyrnauer]] to complete individual portions of the final group project. We primarily communicated through text to clarify homework questions and update progress of the project.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
==References==
LMU BioDB 2017. (2017). Week 12. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

{{Bhamilton18}}

Bhamilton18 Week 12

2017-11-21T02:09:42Z

Bhamilton18: Added Milestone work 0-2

Bhamilton18 Week 12

2017-11-21T01:48:45Z

Bhamilton18: Created page with template and titles

==Electronic Notebook==

==Acknowledgments==
#For this week's assignment I collaborated with my group members, [[User:Zvanysse|Zachary Van Ysseldyk]], [[User:kwrigh35|Katie Wright]] and [[User:Emmatyrnauer|Emma Tyrnauer]] to complete individual portions of the final group project. We primarily communicated through text to clarify homework questions and update progress of the project.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
==References==
LMU BioDB 2017. (2017). Week 12. Retrieved November 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12

{{Bhamilton18}}

Lights, Camera, InterACTION!

2017-11-20T05:42:10Z

Bhamilton18: Added other project page tabs for future ease

Lights, Camera, InterACTION!

2017-11-14T07:35:32Z

Bhamilton18: Executive Summary Addition

Zvanysse Week 11

2017-11-14T06:32:52Z

Bhamilton18: Powerpoint Presentation Added to the page!

==10 Terms==
#Uptime rate: Uptime is a computer industry term for the time during which a computer is operational. (Rouse, 2005)
#Supercomputers: A Supercomputer is a high performance computing machine designed to have extremely fast processing speeds. (Christensson, 2009)
#Gantt chart: A Gantt Chart, commonly used in project management, is one of the most popular and useful ways of showing activities (tasks or events) displayed against time. (What is a Gantt Chart, 2017)
#Agile software: favors small, cross-disciplinary teams that stay in close communication with each other while quickly finishing iterative improvements to a product (Robinson, 2015)
#The Tech Surge: A group of Silicon Valley developers who rescued the website from disorganized contractors and bureaucratic mismanagement. (Robinson, 2015)
#Client software: The software that acts as the interface between the client computer an the server. (Christensson, 2006)
#The waterfall: A sequential design strategy. A central calendar - the Gantt chart to end all Gantt charts. (Robinson, 2015)
#Responsive (In terms of Web Design): This is a type of web design that provides a customized viewing experience for different browser platforms. (Christensson, 2013)
#Cloud: The term "cloud"comes from early network diagrams, in which the image of a cloud was used to indicate a large network, such as a WAN. (Christensson, 2012)
#Static Website: A static website contains Web Pages with fixed content. Each page is coded in HTML and displays the same information to every visitor. (Christensson, 2009)

==Term References==
#Rouse, Margaret. "What is Uptime and Downtime?" ''WhatIs.com'', Sept. 2005, whites.techtarget.com/definition/uptime-and-downtime.
#Christensson, P. (2009, September 25). ''Supercomputer Definition.'' Retrieved 2017, Nov 10, from https://techterms.com
#"What is a Gantt Chart?" ''Gantt'', 2017m www.gantt.com/
#Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 10, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup-saved-healthcare-gov-the-worst-website-in-america/397784/
#Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 10, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup-saved-healthcare-gov-the-worst-website-in-america/397784/
#Christensson, P. (2006). ''Client Definition.'' Retrieved 2017, Nov 10, from https://techterms.com
#Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 10, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup-saved-healthcare-gov-the-worst-website-in-america/397784/
#Christensson, P. (2013, August 20). ''Responsive Web Design Definition.'' Retrieved 2017, Nov 10, from https://techterms.com
#Christensson, P. (2012, May 30). ''Cloud Definition.'' Retrieved 2017, Nov 10, from https://techterms.com
#Christensson, P. (2009, June 12). ''Static Website Definition.'' Retrieved 2017, Nov 10, from https://techterms.com

==Outline==
===Overall Main Message===
*'''Different styles of thinking lead to better and more cost efficient results'''
===The Introduction===
*Healthcare.gov was extremely slow and buggy and needed to be fixed.
===The Problems===
*Site's uptime rate is 91%
*On Healthcare.gov’s first day, six people successfully used it to sign up for health insurance.
*The website was costing hundreds of millions of dollars
*The login requests were taking 2-10 seconds
*'''This sparked the Tech Surge - the beginning of the Marketplace Lite'''
===MarketPlace Lite Birth===
*From the problems noted above, MarketPlace Lite was born
*The goal was to fix all of the problems stated above as well as:
**reduce the cost by 1/50th of the current cost
**reduce the healthcare signup process by half
**Implement new login system which would cost much less as well as not be as problematic
**Rewrite infrastructure for website
===The Process===
*The work life balance was very difficult - ten hours a day, 7 days a week
*Worked at the DoubleTree
*Utilized Amazon Web Services
**A Data center of supercomputers
**Companies can rent out the computational power of these supercomputers at a relatively cheap price as well as makes database management easier
**Can easily scale up or scale back
*Process took over 6 months for Healthcare.gov to accept the AWS proposal
*The MPL team utilized Akamai while waiting for AWS, a cloud provider blessed by the government already to start building the foundational/ structural aspects of the website.
*In 2014, contracts were up, but most stayed on and actual quit their other jobs to join this team
*Switched over to Chat Client help support, this eliminated the long long chains of emails
*The government tried to implement a sequential infrastructure project management approach which ultimately failed
**It basically only wanted to move on when the software was fully implemented using a step by step process which unnecissarily prolonged the project
**They ultimately went the "agile" way, working on multiple things at once
*Tension still rose between Government and MPL because the Government didn't understand what the MPL team was doing
*Eventually, the MPL team released the App and it had great success - as it only took 9 minutes to sign up
*Then, MPL worked on the actual website. They worked out all the bugs relatively quickly because they didn't have the Government breathing down their back
===Significance of this work===
*Made one of the governments' worst websites extremely more efficient and cost effective
*Demonstrated the importance of dedication and hard work and how it pays off
*Shows how alternative ways of thinking lead to better efficiency
===Main Points of Process===
*Outsources to Amazon Web Services
*Switched to Chat Client help support to eliminate long email chains
*Implemented fluid and "agile" philosophy to workflow
*Finished App 2.0 which took customers only 9 minutes to complete
*Reduced login request times to 30 milliseconds from 2-10 seconds
*Reduced cost from 250 million to build and 70 million to maintain to 4 million to build and 1 million to maintain
*Good to have designer in the beginning of project
*Smaller teams work better than bigger teams - better communication
===Takeaways to my assignment===
*Communicate and understand that not all parts of the team have the same knowledge base as one another
*Dynamically work on parts instead of waiting for one group to finish there part
*Different thinking styles are encouraged and lead to better results
*Design the workflow before actually implementing - have a designer

===Powerpoint===
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]

==Acknowledgments==
*I Acknowledge Blair for helping me write out the presentation when consolidating our outlines
*'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 11:15, 13 November 2017 (PST)
==References==
*https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11

==Links==
{{Template:Zvanysse}}

Lights, Camera, InterACTION!

2017-11-14T03:21:07Z

Bhamilton18: Added Powerpoint

[[File:PugNotDrugsLogo.png|400px|thumb|right|Pugs Not Drugs Logo]]

==Team Members==
*[[user:bhamilton18|Blair Hamilton]]
*[[user:emmatyrnauer|Emma Tyrnauer]]
*[[user:kwrigh35|Katie Wright]]
*[[user:zvanysse|Zach Van Ysseldyke]]

==Executive Summaries==

===Week 11===
====Katie - PM/QA====
====Emma - Data Analysis====
====Blair - Coder====
====Zach - Coder====
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]



==Bibliography==

{{template:Pugs Not Drugs}}

Bhamilton18 Week 11

2017-11-14T03:19:32Z

Bhamilton18: Added Powerpoint

==Definitions==
#'''Uptime rate:''' "time during which a piece of equipment (such as a computer) is functioning or able to function."
#*Merriam-Webster’s collegiate dictionary (10th ed.). (1999)
#*https://www.merriam-webster.com/dictionary/uptime
#'''Infrastructure:''' "the underlying foundation or basic framework (as of a system or organization)."
#*Merriam-Webster’s collegiate dictionary (10th ed.). (1999)
#*https://www.merriam-webster.com/dictionary/infrastructure
#'''AWS:''' "Amazon Web Services (AWS) is a secure cloud services platform, offering compute power, database storage, content delivery and other functionality to help businesses scale and grow."
#*What is AWS? - Amazon Web Services. About Page
#*https://aws.amazon.com/what-is-aws/
#'''Cloud Computing:''' "Cloud computing is the on-demand delivery of compute power, database storage, applications, and other IT resources through a cloud services platform via the internet with pay-as-you-go pricing."
#*What is AWS? - Amazon Web Services. About Page
#*https://aws.amazon.com/what-is-cloud-computing/?nc2=h_l2_cc
#'''Domain-name routing:''' It begins with a Domain Name System which "is a directory used by SMTP to convert a name to a list of servers that can receive connections for that name and to find the IP address of a specific server."
#*The Domain Name System (DNS) and SMTP mail routing.
#*https://www.ibm.com/support/knowledgecenter/en/SSKTMJ_9.0.1/admin/plan_thedomainnamesystemdnsandsmtpmailrouting_c.html
#'''Akamai:''' "is the global leader in Content Delivery Network (CDN) services, making the Internet fast, reliable and secure for its customers."
#*About Akamai.
#*https://www.akamai.com/us/en/about/
#'''Sequential design strategy:''' "are iterative algorithms that use data acquired from previous iterations to guide future sample selection."
#*Crombecq, K., Tommasi, L. D., Gorissen, D., & Dhaene, T. (2009)
#*http://ieeexplore.ieee.org/document/5429687/
#'''Gantt chart:''' "A general production planning tool for scienti- fically managed factories."
#*Wilson, James M. (2003)
#*https://web.archive.org/web/20131126152919/http://www-public.it-sudparis.eu/~gibson/Teaching/CSC7003/ReadingMaterial/Wilson03.pdf
#'''Agile-strategy:''' "is proposed in response to the circumstances as a solution and is perceived as a vital characteristic that manufacturing companies need to have in order to maintain their competitive advantages in the new order of world business"
#*H. Sharifi, Z. Zhang, (2001)
#*http://www.emeraldinsight.com/doi/full/10.1108/01443570110390462
#'''Tech Surge:''' "The Obama administration says this surge is made up of engineers from inside and outside government" that are employed to "clean up the code of the error-plagued HealthCare.gov site."
#*Hu, E. (2013, October 21).
#*https://www.npr.org/sections/alltechconsidered/2013/10/22/239220962/the-healthcare-gov-tech-surge-is-racing-against-the-clock
==''The Secret Startup That Saved the Worst Website in America'' '''''Outline'''''==
===Main Message===
#'''It is important to be adaptable when creating a project, as plans and goals change throughout the process.'''
#'''Keeping an open mind, with many difference perspectives allows the project to run more smoothly and effectively.'''
===Introduction===
#HealthCare.gov was a website implemented during the Obama Administration to enforce the Affordable Care Act.
#The website has a "start-up" atmosphere, but was being maintained by government officials who didn't understand start-ups.
#The website needed a larger makeover, and therefore teams were brought in to fix the site.
===The Problem===
#The US government attempted to create a HealthCare.gov website in order for citizens to find and sign up for health care.
#HealthCare.gov became one of the worst websites for users.
#*'''91% uptime rate'''
#*'''Six successful sign ups on the first day'''
#**'''Despite thousands attempting'''
#*'''$250 million to build'''
#*'''$70 million maintain'''
===The Need===
#Technical Workers who could quickly to fix, maintain and reduce costs of the Healthcare.gov website
#*This created a '''Tech Surge''' which was a group of Silicon Valley developers who needed to "save" the website.
#Althoguh the '''Tech Surge''' received the most spotlight, it was a group called Marketplace Lite that dealt with the nitty-gritty of HealthCare.gov.
#*'''Marketplace Lite''' was a a group of designers and developers that worked round the clock to create a working, successful health care tool.
===The Process===
#Marketplace Lite was a small group of start up coders whose work started at the Doubletree Hotel in Baltimore.
#The MPL (Marketplace Lite) was set up for days in the dining rooms, floors and lobby of the hotel.
#The days consisted of 10hours a day 7 days a week for months.
#The MPL wanted to create a more efficient way to store and manage the data that came with the HealthCare.gov website.
#*This prompted the MPL workers to reach out to cheaper storage options, such as '''Amazon Web Services (AWS)'''.
#**AWS allows for users to rent storage or computational power more cheaply than running/storing on the users own.
#***By utilizing off site super computers, AWS can increase runtime, decrease cost and scale the computational power to the demand of the consumer.
#**The AWS platform was not accepted by the government for many months, therefore as a place holder '''Akami''' was used.
#***AWS was approved nearly six months later in the process.
#By 2014, the members in the MPL team and Tech Surge projects contact's were running out. While the Tech Surge group was disbanding many members in the MPL team stayed on the project and even quit their "day-jobs."
#*One person left Google, one left SkillShare
#*New members were hired with start up experience to help the project continue smoothly.
#Once the Tech Surge had completed, MPL moved from the DoubleTree lobby to the CMS offices.
#*However, this just meant when employees would leave their desks for meetings or breaks, MPL members would "borrow" their desks for a short period of time.
#Once the summer began, MPL looked for a stable office space, which led them to rent a house in suburban Maryland.
#*The house was made up of a few beds and lots of cheap furniture.
#*The house was purely a cheap space to eat, sleep and work.
#One important piece of tech that dramatically increased the MPL work efficiency was the implementation of '''HipChat'''
#*'''HipChat''' is a group chatroom, much like Slack, that allows quick messages and attachments to be sent and reviewed more efficiently than email.
#Preceding the implementation of HipChat the government began forcing deadlines and work environment regulations.
#*This included creating a detailed 3-month plan for the coders to follow, despite accepting the "agile" way for working.
#**As defined above, the "agile" way of working is more effective, especially for programers, developers and designers as it allows flexibility with project deadlines and adjustment for errors.
#*The government wanted to control every aspect of the website despite not understanding how it or the programmer plan worked.
#With time, the government learned that the programmers "knew what they were doing" and followed the launch plan of '''App 2.0'''
#*'''App 2.0''' is the MPL insurance application that allowed users to sign up and in more quickly than the original application.
#**Users could finish in '''9 minutes''' versus the original '''20 minutes'''
#**Users only had to go through '''16 pages''' instead of '''76 pages'''
#**A record '''85%''' of users were able to finish the registration versus the previous '''55%.'''
#**Login request times reduced to 30 milliseconds instead of 2-10 seconds
#The MPL team decided to release App 2.0 in stages:
#*0% to users
#*10% to users
#*20% to users
#*All the way to 100%
#*These stages meant the develop and bug fixes could be more manageable rather than other loading the team members and the servers.
#In the end, MPL made a terrific website that saved time, energy and money for the government.
#Although the team has disbanded, they have since created a new corporation called Nava, to help the government for future "start-up opportunities."
===Significance===
#Changed HealthCare.gov for the better by making it cost effective, efficient and easy to use.
#Emphasizes the importance of small, but effective group work.
#Developers and designers need to present from the begin to ensure the knowledge of the features versus needs is explicit.
#Displays how new perspectives and work environment styles can make a project go smoother.
===Main Process Points===
#HipChat was extremely helpful to send attachments and exchange communication quickly and effectively.
#AWS/Akamai were cost effective programs that were able to store data off site and allow the runtime to increase in efficiency.
#App 2.0, or the insurance application, was an easy way to break up the project into manageable pieces.
#*App 2.0 allowed for the user sign in/registering to go quickly and actually work!
===Applications to our Project===
#As I mentioned in my class journal last week, communication is going to be a big part of how the project will go smoothly.
#*Utilizing apps like Slack or even messenger with my coding parter Zach will allow us to work independently, but also collaborate quickly when needed.
#Adapting the '''agile''' strategy our group will be able to set realistic goals and adjust for road blocks.
#In working with all the members of the group from the beginning, it will allow project updates and features to be discussed from the beginning.
#*In talking with Katie, I will be able to voice any issues, successes or delays with her so she isn't surprised as a Project Manager is a deliverable isn't going according to plan.
==Presentation==
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]
==Acknowledgments==
#I worked with my group project coding partner [[User: Zvanysse | Zachary Van Ysseldyk]] on our presentation as well as formatting outlines similarly. We met in person as well as through Google slides to collaborate on the presentation.
#I worked with other fellow group members: [[User:kwrigh35|Katie Wright]] and [[User:Emmatyrnauer|Emma Tyrnauer]] to consult on our team project page and formatting.
#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
==Term References==
#About Akamai.Retrieved November 11, 2017, from https://www.akamai.com/us/en/about/
#Crombecq, K., Tommasi, L. D., Gorissen, D., & Dhaene, T. (2009). A novel sequential design strategy for global surrogate modeling. Proceedings of the 2009 Winter Simulation Conference (WSC). doi:10.1109/wsc.2009.5429687
#The Domain Name System (DNS) and SMTP mail routing. Retrieved November 11, 2017, from https://www.ibm.com/support/knowledgecenter/en/SSKTMJ_9.0.1/admin/plan_thedomainnamesystemdnsandsmtpmailrouting_c.html
#H. Sharifi, Z. Zhang, (2001) "Agile manufacturing in practice ‐ Application of a methodology", International Journal of Operations & Production Management, Vol. 21 Issue: 5/6, pp.772-794, https://doi.org/10.1108/01443570110390462
#Hu, E. (2013, October 21). The HealthCare.gov 'Tech Surge' Is Racing Against The Clock. Retrieved November 11, 2017, from https://www.npr.org/sections/alltechconsidered/2013/10/22/239220962/the-healthcare-gov-tech-surge-is-racing-against-the-clock
#Merriam-Webster’s collegiate dictionary (10th ed.). (1999). Springfield, MA: Merriam-Webster Incorporated.
#What is AWS? - Amazon Web Services. Retrieved November 11, 2017, from https://aws.amazon.com/what-is-aws/
#Wilson, James M. (2003). "Gantt charts: A centenary appreciation" (PDF). European Journal of Operational Research. 149 (2): 430–437. doi:10.1016/S0377-2217(02)00769-5. Archived from the original (PDF) on 26 November 2013.
==References==
#LMU BioDB 2017. (2017). Week 10. Retrieved November 7, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup-saved-healthcare-gov-the-worst-website-in-america/397784/

{{Bhamilton18}}

File:The Secret Startup that Saved the Worst Website in America.pdf

2017-11-14T03:17:30Z

Bhamilton18: Presentation Powerpoint with Zach

Presentation Powerpoint with Zach