LMU BioDB 2017 - User contributions [en]

Lights, Camera, InterACTION!

2017-12-15T05:26:49Z

Zvanysse: zachs exec 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====
This week I completed last steps for data analysis including the visualization of my gene network in GRNsight. Specifics of steps performed and associated files can be accessed on [[Emmatyrnauer Week 15]]. I also met up with my teammates prior to the presentation to complete the powerpoint as well as practice a few times. Once the presentation was complete, our entire group communicated over text to finish the final deliverables for this project (i.e. the group report, individual statements, etc.) I was really happy with how things turned out!

[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 18:01, 14 December 2017 (PST)

====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====
This week was mainly focused on pulling together all the coder's code for major integrations. [[User:Bhamilton|Blair]] and I inputed all the data pulled from the API team to integrate into the HTML file so the page designers could see their final product. The integration team all worked on the presentation together in person. We communicated through texting, calling, and meeting up in person. More information can be found on our electronic notebooks, but overall the project was completed. If any other teams make major changes which mess with the integration teams website, I will be on call until the deadline on Friday at 4:30.

[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 21:26, 14 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

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{{GRNsight Gene Page Project Links}}

Zvanysse Week 15

2017-12-15T04:31:07Z

Zvanysse: Finishing touches

===Notebook for Week 15===
#As the teams were finishing up their code, we worked on major integrations from JASPAR, Gene Database APIs, and Page Design teams.
#It was difficult to communicate with certain teams on integrating, but once it was escalated it was resolved to a level in which we were able to complete our tasks on time.
#Specifically, we added NCBI, SGD, Ensemble, Uniprot, and JASPAR ID's to the top of the page.
#Through communication with Dondi,we found the correct ID format on how to reference the info.html and api.js file.
#*'''Below is how the code looks:'''
#*<code>var ncbiHrefTemplate = "https://www.ncbi.nlm.nih.gov/gene/"; </code>
#**Above is a template version for the genes information that comes from NCBI, now we can tag the unique gene to the template pathway as follows:
#*<code>var ncbiId = gene.ncbi.ncbiID;</code>
#**So the above code extends the pathway to find the ncbi ID for the specific gene.
#*<code>$(".ncbi-link").text(ncbiId).attr({ href: ncbiHrefTemplate + ncbiId });</code>
#**The "$" references the query api. Basically, this above line of code strings together the code adding the template and the specific part together.
#*We had to link the data from the api.js file to where the page design team wanted the data in the info.html file
#We made each ID and built a skeleton so that once the api calls were all situated, it wouldn't be a problem once they lock down the correct path.
#*Currently we have all the data being correctly pulled.
#*For HMO1, for example, this is what the heading looks like:
#*[[File:GeneIDs.png|500px|thumb|center|HMO1 Gene Page Title]]
#Once we saw this working, we took the majority of the code and replicated it for the other data fields
#We ran into trouble when trying to input the frequency matrix because the for the other page, we were using P-tags, but for this frequency matrix, we had to implement it another way.
#*Initially we had some problems so we consulted our good friends Dr. Dionisio and the Eddies who helped us with the formatting of the table.
#*because the length was not a set in stone length, we used a for loop to circumnavigate the unknown length. Find the code below:
#*'''Frequency matrix code:'''
#**<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>
#*We also had trouble with the actual implantation of the logo. We quickly found out that a src tag is supposed to be used to link between the API call thanks to Dondi. Eddie B. Also helped us with explaining how to retrieve the image URL.
#*'''Specifically this can be seen here:'''
#**<code>var sequenceLogo = gene.jaspar.sequenceLogo;</code>
#**<code>$(".sequenceLogo").attr({ src : sequenceLogo });</code>
#This is an example of the Frequency Matrix and Sequence Logo for ASH1:
#*[[File:MatrixPic.png|500px|thumb|center|Fequency Matrix and Sequence Logo --- ASH1 Gene]]
#Now that all the data has been linked and integrated, collaboration with the page design team and other biologists will help format the page to look aesthetically pleasing.
#For now, this is the current design for the HOT1 page:
#*[[File:Infohtmlpic.png|600px|thumb|center|GRNsight Gene Page for HOT1]]

==Team Deliverable Progress==
Overall, this week was primarily focused on wrapping up the code and finalizing the presentation. The presentation was practiced and rehearsed by all of us when we met in person. Katie focused heavily on the presentation aesthetic as well as making sure that she understood everything that was going on so that she would be able to help as needed. Emma finalized her data analysis portion. We all worked together on putting together the powerpoint presentation and made sure that each person had enough time to speak. As for the actual deliverables, the final pulls will be done before Friday 15th. If any major integration problems arise from last minute changes due to other teams, we will be on standby to make sure it is all worked out. The paper has been in the works with all of us contributing.

===Acknowledgments===
#I worked with Blair Hamilton to collaborate on the integration portion of our assignment. We met up in person as well as communicated through texting.
#We worked with Dr. Dionisio for figuring out the id Syntax and class references.
#We acknowledge the teams of JASPAR, Gene Database APIs, and Page Design throughout integrations.
#Collaborated with [[User:ebachour|Eddie Bachoura]] on creating a table/for-loop for the frequency matrix portion of the info.html page. (thanks so much)
#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 Blair and I 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:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 11:26, 13 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

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Zvanysse Week 15

2017-12-15T04:12:32Z

Zvanysse: adding electronic notebook

===Notebook for Week 15===
#As the teams were finishing up their code, we worked on major integrations from JASPAR, Gene Database APIs, and Page Design teams.
#It was difficult to communicate with certain teams on integrating, but once it was escalated it was resolved to a level in which we were able to complete our tasks on time.
#Specifically, we added NCBI, SGD, Ensemble, Uniprot, and JASPAR ID's to the top of the page.
#Through communication with Dondi,we found the correct ID format on how to reference the info.html and api.js file.
#*'''Below is how the code looks:'''
#*<code>var ncbiHrefTemplate = "https://www.ncbi.nlm.nih.gov/gene/"; </code>
#**Above is a template version for the genes information that comes from NCBI, now we can tag the unique gene to the template pathway as follows:
#*<code>var ncbiId = gene.ncbi.ncbiID;</code>
#**So the above code extends the pathway to find the ncbi ID for the specific gene.
#*<code>$(".ncbi-link").text(ncbiId).attr({ href: ncbiHrefTemplate + ncbiId });</code>
#**The "$" references the query api. Basically, this above line of code strings together the code adding the template and the specific part together.
#*We had to link the data from the api.js file to where the page design team wanted the data in the info.html file
#We made each ID and built a skeleton so that once the api calls were all situated, it wouldn't be a problem once they lock down the correct path.
#*Currently we have all the data being correctly pulled.
#*For HMO1, for example, this is what the heading looks like:
#*[[File:GeneIDs.png|500px|thumb|center|HMO1 Gene Page Title]]
#Once we saw this working, we took the majority of the code and replicated it for the other data fields
#We ran into trouble when trying to input the frequency matrix because the for the other page, we were using P-tags, but for this frequency matrix, we had to implement it another way.
#*Initially we had some problems so we consulted our good friends Dr. Dionisio and the Eddies who helped us with the formatting of the table.
#*because the length was not a set in stone length, we used a for loop to circumnavigate the unknown length. Find the code below:
#*'''Frequency matrix code:'''
#**<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>
#*We also had trouble with the actual implantation of the logo. We quickly found out that a src tag is supposed to be used to link between the API call thanks to Dondi. Eddie B. Also helped us with explaining how to retrieve the image URL.
#*'''Specifically this can be seen here:'''
#**<code>var sequenceLogo = gene.jaspar.sequenceLogo;</code>
#**<code>$(".sequenceLogo").attr({ src : sequenceLogo });</code>
#This is an example of the Frequency Matrix and Sequence Logo for ASH1:
#*[[File:MatrixPic.png|500px|thumb|center|Fequency Matrix and Sequence Logo --- ASH1 Gene]]

===Acknowledgments===
#I worked with Blair Hamilton to collaborate on the integration portion of our assignment. We met up in person as well as communicated through texting.
#We worked with Dr. Dionisio for figuring out the id Syntax and class references.
#We acknowledge the teams of JASPAR, Gene Database APIs, and Page Design 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:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 11:26, 13 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

{{Template:Zvanysse}}

Zvanysse Week 15

2017-12-13T19:26:43Z

Zvanysse: Made workbook

Template:Zvanysse

2017-12-13T19:13:42Z

Zvanysse:

Zvanysse Week 12

2017-12-13T19:11:35Z

Zvanysse: tidied up

==Electronic Notebook==
For this week's assignment [[User:Bhamilton18|Blair Hamilton]] and I worked on the [[Coder]] Milestones 0-4. Blair and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website.

===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===
#First, we had to make sure that the required software was downloaded correctly
#The following softwares were downloaded to my computer so the milestone could be completed:
#* Node.js 8.4.0
#* Code text editor (Sublime, in my case)
#* Web browser with developer tools (Chrome for my case)
#* '''git''' version control software
#* '''curl''' command

===Milestone 2===
#This portion required us 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.
#We 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 Blair's 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 Sublime.
#* '''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:BHamilton18|Blair Hamilton]], [[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.
#Blair helped me a lot with understanding what forking and branching meant. I collaborated with her on how to format the electronic notebook above.
#'''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

{{Template:Zvanysse}}

Zvanysse Week 14

2017-12-13T19:06:31Z

Zvanysse: Fixed potential plagiarism

==Electronic Lab Notebook==
This week [[User:Bhamilton18|Blair Hamilton]] and I worked on the Coder portion of our Interaction and Integration section for the final project.
#In the beginning we held a group meeting to measure the progress of each member in the group.
#We (Blair and I) also met with Dondi in order to work on syntax for our coding part of the assignment.
#We first wanted to have the user '''right''' click on any of the genes from the genes on the GRNSight gene map interactive visualization page to open up into a new tab.
#*Because we just needed a template, we used this weskit to link to the page: [http://dogtime.com/dog-breeds/pug#/slide/1] (Blair influenced this decision because of her love for Dogs)
#*Again, we just wanted a working template so we could start focusing in on the skeleton to stage our code to be able to easily input the other team's code.
#We then wanted to create a simple web page similar to our gene page so the page could link to an internal link rather than an external one
#*One of the biggest challenges was that the browser denied requests to go to another page for potential security breach reasons. So, we asked Dondi and he created a fake anchor so that we could have a landing page, then put the URL on that landing page, then took the landing page away.
#*The problem is not fixed in its entirety but it has been realized.
# href: "/gene/info.html?" + $.param({symbol: gene.name}),
#* First, the "/gene/info.html?" part of the code allows the right click to go to a template page called info.html
#*Next the parameters specifies the pathway to go to the gene that was selected by the user
#**Example: if "BRO1" is right clicked from GRNSight, the new page will console.log the gene name.
#Finally we merged the other groups work through GitHub for the first integration. All went well and we will be collaborating more with groups soon.

==Acknowledgements==
#I worked with [[User:Bhamilton18|Blair Hamilton]] 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===
*Get url parameter jquery Or How to Get Query String Values In js. (n.d.). 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? (n.d.). Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
*JavaScript Window Location. (n.d.). Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
*Window.location. (n.d.). Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Template:Zvanysse}}

Lights, Camera, InterACTION!

2017-12-05T05:36:07Z

Zvanysse: uploaded week 14 zvanysse

[[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====
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}}

Zvanysse Week 14

2017-12-05T05:20:59Z

Zvanysse: fixed linking

==Electronic Lab Notebook==
This week [[User:Bhamilton18|Blair Hamilton]] and I worked on the Coder portion of our Interaction and Integration section for the final project.
#In the beginning we held a group meeting to measure the progress of each member in the group.
#We (Blair and I) also met with Dondi in order to work on syntax for our coding part of the assignment.
#We first wanted 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 was that Safari and Chrome believe the websites are pop-ups and therefore blocks them. We were having some problems because some of the syntax changed, so Dondi worked his magic and created a fake anchor and made it invisible then linked the page so the right click button worked.
#*We have not fixed this problem yet but we have noted.
# 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:Bhamilton18|Blair Hamilton]] 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===
*Get url parameter jquery Or How to Get Query String Values In js. (n.d.). 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? (n.d.). Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
*JavaScript Window Location. (n.d.). Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
*Window.location. (n.d.). Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Template:Zvanysse}}

Zvanysse Week 14

2017-12-05T05:12:59Z

Zvanysse: updated electronic workbook

==Electronic Lab Notebook==
This week [[User:BHamilton18|Blair Hamilton]] and I worked on the Coder portion of our Interaction and Integration section for the final project.
#In the beginning we held a group meeting to measure the progress of each member in the group.
#We (Blair and I) also met with Dondi in order to work on syntax for our coding part of the assignment.
#We first wanted 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 was that Safari and Chrome believe the websites are pop-ups and therefore blocks them. We were having some problems because some of the syntax changed, so Dondi worked his magic and created a fake anchor and made it invisible then linked the page so the right click button worked.
#*We have not fixed this problem yet but we have noted.
# 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:BHamilton18|Blair Hamilton]] 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===
*Get url parameter jquery Or How to Get Query String Values In js. (n.d.). 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? (n.d.). Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
*JavaScript Window Location. (n.d.). Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
*Window.location. (n.d.). Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location

{{Template:Zvanysse}}

Zvanysse Week 14

2017-12-05T04:54:05Z

Zvanysse: updated references

===References===
*How to retrieve GET parameters from javascript? (n.d.). Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
*Window.location. (n.d.). Retrieved December 04, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Window/location
*JavaScript Window Location. (n.d.). Retrieved December 04, 2017, from https://www.w3schools.com/js/js_window_location.asp
*Get url parameter jquery Or How to Get Query String Values In js. (n.d.). Retrieved December 04, 2017, from https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js

Class Journal Week 14

2017-12-05T02:16:11Z

Zvanysse: /* References */

Class Journal Week 14

2017-12-05T02:09:46Z

Zvanysse: /* References */

===References===
*How to retrieve GET parameters from javascript? (n.d.). Retrieved December 04, 2017, from https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
*https://developer.mozilla.org/en-US/docs/Web/API/Window/location
*https://www.w3schools.com/js/js_window_location.asp
*https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js

Class Journal Week 14

2017-12-04T00:31:44Z

Zvanysse: Added references

===References===
*https://stackoverflow.com/questions/5448545/how-to-retrieve-get-parameters-from-javascript
*https://developer.mozilla.org/en-US/docs/Web/API/Window/location
*https://www.w3schools.com/js/js_window_location.asp
*https://stackoverflow.com/questions/19491336/get-url-parameter-jquery-or-how-to-get-query-string-values-in-js

Template:Zvanysse

2017-12-04T00:24:46Z

Zvanysse:

Template:Zvanysse

2017-12-04T00:17:32Z

Zvanysse:

Lights, Camera, InterACTION!

2017-11-21T03:21:11Z

Zvanysse:

Lights, Camera, InterACTION!

2017-11-21T03:00:46Z

Zvanysse:

Zvanysse Week 12

2017-11-21T02:46:55Z

Zvanysse: Updating milestones

==Electronic Notebook==
For this week's assignment [[User:BHamilton18|Blair Hamilton]] and I worked on the [[Coder]] Milestones 0-4. Blair and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website.

===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 us 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 Blair's 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:BHamilton18|Blair Hamilton]], [[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.
#Blair helped me a lot with understanding what forking and branching meant. I collaborated with her on how to format the electronic notebook above.
#'''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

{{Template:Zvanysse}}

Zvanysse Week 12

2017-11-21T02:41:54Z

Zvanysse: Created page with "==Electronic Notebook== For this week's assignment Blair Hamilton and I worked on the Coder Milestones 0-4. Blair and I will be working on the integr..."

==Electronic Notebook==
For this week's assignment [[User:BHamilton18|Blair Hamilton]] and I worked on the [[Coder]] Milestones 0-4. Blair and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website.

===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 us 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 Blair's 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:BHamilton18|Blair Hamilton]], [[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.
#Blair helped me a lot with understanding what forking and branching meant. I collaborated with her on how to format the electronic notebook above.
#'''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

{{Template:Zvanysse}}

Template:Zvanysse

2017-11-21T02:24:37Z

Zvanysse:

Lights, Camera, InterACTION!

2017-11-14T07:44:14Z

Zvanysse: updated my executive summary

Zvanysse Week 11

2017-11-13T19:15:38Z

Zvanysse: added links and references

==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

==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}}

Zvanysse Week 11

2017-11-13T18:39:27Z

Zvanysse: updated outline

Zvanysse Week 11

2017-11-13T18:19:48Z

Zvanysse: updating outline

==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.
*'''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 scan 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, which they worked out all the bugs for 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
===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

Zvanysse Week 11

2017-11-13T18:17:08Z

Zvanysse: updating outline

==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.
*'''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 scan 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, which they worked out all the bugs for relatively quickly because they didn't have the Government breathing down their back
===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
===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

Zvanysse Week 11

2017-11-13T17:21:18Z

Zvanysse:

==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==
===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.
*'''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 scan 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, which they worked out all the bugs for relatively quickly because they didn't have the Government breathing down their back
===Main Points of Process===

Zvanysse Week 11

2017-11-13T17:11:13Z

Zvanysse: Updating outline

Zvanysse Week 11

2017-11-13T08:32:24Z

Zvanysse: Updating outline

Zvanysse Week 11

2017-11-12T07:14:16Z

Zvanysse: updating terms

Zvanysse Week 11

2017-11-11T05:47:22Z

Zvanysse:

Zvanysse Week 11

2017-11-11T04:49:27Z

Zvanysse: updating more terms/definitions

Zvanysse Week 11

2017-11-11T04:37:30Z

Zvanysse: Updating term definitions

Zvanysse Week 11

2017-11-11T04:13:23Z

Zvanysse: adding term references/ definitions

==10 Terms==
#Uptime rate: Uptime is a computer industry term for the time during which a computer is operational. (Rouse, 2005)
#Supercomputers
#Gantt chart
#Login System
#The Tech Surge
#Chat client
#The waterfall
#Responsive (In terms of application development)
#Cloud Storage
#Static Website

==Term References==
#Rouse, Margaret. "What is Uptime and Downtime?" ''WhatIs.com'', Sept. 2005, whites.techtarget.com/definition/uptime-and-downtime.

Zvanysse Week 11

2017-11-07T23:46:30Z

Zvanysse: started looking for terms

==10 Terms==
#uptime rate
#supercomputers
#Gantt chart
#

Template:Zvanysse

2017-11-07T23:36:07Z

Zvanysse:

Template:Zvanysse

2017-11-07T23:35:40Z

Zvanysse:

Zvanysse Week 10

2017-11-05T23:59:10Z

Zvanysse: Updating acknowledgments and References

==== Clustering and GO Term Enrichment with stem ====

# '''Prepare your microarray data file for loading into STEM.'''
#* Download your Excel workbook that you used for your [[Week 8]] assignment.
#* Insert a new worksheet into your Excel workbook, and name it "dGLN3_stem".
#* Select all of the data from your "dGLN3_ANOVA" worksheet and Paste special > paste values into your "dGLN3_stem" worksheet.
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise. '''''Record the number of genes left in your electronic notebook.'''''
#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
#** Save your work. Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
#*** Note that you should turn on the file extensions if you have not already done so.
# '''Now download and extract the STEM software.''' [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
#* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
#* Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
#* This will create a folder called <code>stem</code>. Inside the folder, double-click on the <code>stem.jar</code> to launch the STEM program.

# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
##* Click on the radio button ''No normalization/add 0''.
##* Check the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, select ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. Select ''No cross references'', from the Cross Reference Source drop-down menu. Select ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) click on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
##* Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
##*Take a screenshot of this window (on a PC, simultaneously press the <code>Alt</code> and <code>PrintScreen</code> buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.
## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
# '''Analyzing and Interpreting STEM Results'''
## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following:
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##* '''''How many genes belong to this profile?'''''
##* '''''How many genes were expected to belong to this profile?'''''
##* '''''What is the p value for the enrichment of genes in this profile?''''' Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
##* Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
##** Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor that was deleted from your strain?'''''
##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].

==Powerpoint and Zip==
[[Media:StemGraphResults.pptx|dGLN3 Stem Graph Result Powerpoint]] 
[[Media:DGLN3_STEM.zip|DGLN3 Zip File]]

==Electronic Workbook==
*Number of Genes left <0.05 = 1258
*I selected '''Profile 48''' as my desired profile because it showed the clearest pattern at different time points. 55.0 genes belong to this profile and 22.0 genes were expected to belong to profile 48. The p-value for the enrichment of genes in this profile is 2.2 E-9. There are 12 GO terms associated with this profile at p < 0.05 and 0 GO terms associated with this profile with a corrected p value < 0.05.
*6 Definitions:
*#chromosome organization: A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
*#transmembrane transport: The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
*#organelle fission: The creation of two or more organelles by division of one organelle.
*#macromolecule modification: The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.
*#substrate-specific transporter activity: Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
*#meiotic cell cycle process: Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.

==Acknowledgments==
*I acknowledge Dina for helping with the statistical analysis and helping me to understand what the terms meant.
'''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]]) 15:59, 5 November 2017 (PST)

==References==
*http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848
*https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10

Zvanysse Week 10

2017-11-05T23:53:42Z

Zvanysse: /* Electronic Workbook */

==== Clustering and GO Term Enrichment with stem ====

# '''Prepare your microarray data file for loading into STEM.'''
#* Download your Excel workbook that you used for your [[Week 8]] assignment.
#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
#* Select all of the data from your "dGLN3_ANOVA" worksheet and Paste special > paste values into your "dGLN3_stem" worksheet.
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise. '''''Record the number of genes left in your electronic notebook.'''''
#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
#** Save your work. Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
#*** Note that you should turn on the file extensions if you have not already done so.
# '''Now download and extract the STEM software.''' [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
#* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
#* Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
#* This will create a folder called <code>stem</code>. Inside the folder, double-click on the <code>stem.jar</code> to launch the STEM program.

# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
##* Click on the radio button ''No normalization/add 0''.
##* Check the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, select ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. Select ''No cross references'', from the Cross Reference Source drop-down menu. Select ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) click on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
##* Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
##*Take a screenshot of this window (on a PC, simultaneously press the <code>Alt</code> and <code>PrintScreen</code> buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.
## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
# '''Analyzing and Interpreting STEM Results'''
## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following:
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##* '''''How many genes belong to this profile?'''''
##* '''''How many genes were expected to belong to this profile?'''''
##* '''''What is the p value for the enrichment of genes in this profile?''''' Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
##* Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
##** Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor that was deleted from your strain?'''''
##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].

==Powerpoint and Zip==
[[Media:StemGraphResults.pptx|dGLN3 Stem Graph Result Powerpoint]] 
[[Media:DGLN3_STEM.zip|DGLN3 Zip File]]

==Electronic Workbook==
*Number of Genes left <0.05 = 1258
*I selected '''Profile 48''' as my desired profile because it showed the clearest pattern at different time points. 55.0 genes belong to this profile and 22.0 genes were expected to belong to profile 48. The p-value for the enrichment of genes in this profile is 2.2 E-9. There are 12 GO terms associated with this profile at p < 0.05 and 0 GO terms associated with this profile with a corrected p value < 0.05.
*6 Definitions:
*#chromosome organization: A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
*#transmembrane transport: The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
*#organelle fission: The creation of two or more organelles by division of one organelle.
*#macromolecule modification: The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.
*#substrate-specific transporter activity: Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
*#meiotic cell cycle process: Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.

Template:Zvanysse

2017-11-05T21:38:49Z

Zvanysse: update template

Class Journal Week 10

2017-11-05T21:36:22Z

Zvanysse: Zach Van Ysseldyk responses uploaded

=Class Journal Week 10=
==Hayden Hinsch's Responses==

{{hhinsch}}

==Mary Balducci's Responses==
#I would want for my teammates to be available if I have questions about the work, and also to feel like they can ask me questions. I would want us all to share equal amounts of the work, and to be able to get in touch with each other if we need help with something.
#I think communication makes teamwork go smoothly. If we are all able to tell each other what we're working on and how we're doing it, I think it helps everyone better understand the project being done. This also includes being responsive to questions and figuring out who is responsible for each aspect of the project together.
#I think teamwork does not go smoothly when members of the team are not responsive. I think it's harder when I'm not entirely sure what another person in my group is doing, or if I have a question and they are not available to answer it.

[[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 07:44, 3 November 2017 (PDT)

==Zachary Van Ysseldyk's Responses==
#As far as characteristics for a teammate, I value those who do not procrastinate and plan out how the assignment will get done to avoid unnecessary stress. Stringing along the same thought, I think that communication is crucial so that every person on the team is on the same page. I would also value those who assume the same amount of work as everybody else so that we all get a fair and well deserved grade.
#Bleeding in from question 1, I think that solid communication and a laid out plan will help the project go smoothly. Knowing when things will get done and how long they will take will help for smooth project completion.
#On the other hand, poor communication will greatly negatively affect a project. People might be doing the same things, people might not understand what they are doing which leads to frustration and division among the team. Also if somebody does not put in a sufficient amount of effort, this will anger others as the person who didn't do the the work should not receive the same letter grade.
 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 13:36, 5 November 2017 (PST)
 
{{Template:Zvanysse}}

[[Category:Shared]]
[[Category:Journal Entry]]

Zvanysse Week 10

2017-11-03T21:15:00Z

Zvanysse: updating definitions

==== Clustering and GO Term Enrichment with stem ====

# '''Prepare your microarray data file for loading into STEM.'''
#* Download your Excel workbook that you used for your [[Week 8]] assignment.
#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
#* Select all of the data from your "dGLN3_ANOVA" worksheet and Paste special > paste values into your "dGLN3_stem" worksheet.
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise. '''''Record the number of genes left in your electronic notebook.'''''
#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
#** Save your work. Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
#*** Note that you should turn on the file extensions if you have not already done so.
# '''Now download and extract the STEM software.''' [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
#* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
#* Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
#* This will create a folder called <code>stem</code>. Inside the folder, double-click on the <code>stem.jar</code> to launch the STEM program.

# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
##* Click on the radio button ''No normalization/add 0''.
##* Check the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, select ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. Select ''No cross references'', from the Cross Reference Source drop-down menu. Select ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) click on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
##* Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
##*Take a screenshot of this window (on a PC, simultaneously press the <code>Alt</code> and <code>PrintScreen</code> buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.
## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
# '''Analyzing and Interpreting STEM Results'''
## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following:
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##* '''''How many genes belong to this profile?'''''
##* '''''How many genes were expected to belong to this profile?'''''
##* '''''What is the p value for the enrichment of genes in this profile?''''' Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
##* Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
##** Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor that was deleted from your strain?'''''
##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].

==Powerpoint and Zip==
[[Media:StemGraphResults.pptx|dGLN3 Stem Graph Result Powerpoint]] 
[[Media:DGLN3_STEM.zip|DGLN3 Zip File]]

==Electronic Workbook==
*Number of Genes left <0.05 = 1258
*I selected '''Profile 48''' as my desired profile because it showed the clearest pattern at different time points. 55.0 genes belong to this profile and 22.0 genes were expected to belong to profile 48. The p-value for the enrichment of genes in this profile is 2.2 E-9. There are 12 GO terms associated with this profile at p < 0.05 and 0 GO terms associated with this profile with a corrected p value < 0.05.
*6 Definitions:
*#chromosome organization: A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
*#transmembrane transport: The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
*#organelle fission
*#macromolecule modification
*#substrate-specific transporter activity
*#meiotic cell cycle process

Zvanysse Week 10

2017-11-03T20:47:09Z

Zvanysse: working on electronic workbook

==== Clustering and GO Term Enrichment with stem ====

# '''Prepare your microarray data file for loading into STEM.'''
#* Download your Excel workbook that you used for your [[Week 8]] assignment.
#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
#* Select all of the data from your "dGLN3_ANOVA" worksheet and Paste special > paste values into your "dGLN3_stem" worksheet.
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise. '''''Record the number of genes left in your electronic notebook.'''''
#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
#** Save your work. Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
#*** Note that you should turn on the file extensions if you have not already done so.
# '''Now download and extract the STEM software.''' [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
#* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
#* Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
#* This will create a folder called <code>stem</code>. Inside the folder, double-click on the <code>stem.jar</code> to launch the STEM program.

# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
##* Click on the radio button ''No normalization/add 0''.
##* Check the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, select ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. Select ''No cross references'', from the Cross Reference Source drop-down menu. Select ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) click on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
##* Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
##*Take a screenshot of this window (on a PC, simultaneously press the <code>Alt</code> and <code>PrintScreen</code> buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.
## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
# '''Analyzing and Interpreting STEM Results'''
## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following:
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##* '''''How many genes belong to this profile?'''''
##* '''''How many genes were expected to belong to this profile?'''''
##* '''''What is the p value for the enrichment of genes in this profile?''''' Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
##* Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
##** Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor that was deleted from your strain?'''''
##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].

==Powerpoint and Zip==
[[Media:StemGraphResults.pptx|dGLN3 Stem Graph Result Powerpoint]]
[[Media:DGLN3_STEM.zip|DGLN3 Zip File]]

==Electronic Workbook==
*Number of Genes left <0.05 = 1258
*I selected '''Profile 48''' as my desired profile because it showed the clearest pattern at different time points. 55.0 genes belong to this profile and 22.0 genes were expected to belong to profile 48. The p-value for the enrichment of genes in this profile is 2.2 E-9.

Zvanysse Week 10

2017-11-03T20:40:07Z

Zvanysse: uploading zip and instructions

==== Clustering and GO Term Enrichment with stem ====

# '''Prepare your microarray data file for loading into STEM.'''
#* Download your Excel workbook that you used for your [[Week 8]] assignment.
#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
#* Select all of the data from your "dGLN3_ANOVA" worksheet and Paste special > paste values into your "dGLN3_stem" worksheet.
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise. '''''Record the number of genes left in your electronic notebook.'''''
#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
#** Save your work. Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
#*** Note that you should turn on the file extensions if you have not already done so.
# '''Now download and extract the STEM software.''' [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
#* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
#* Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
#* This will create a folder called <code>stem</code>. Inside the folder, double-click on the <code>stem.jar</code> to launch the STEM program.

# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
##* Click on the radio button ''No normalization/add 0''.
##* Check the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, select ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. Select ''No cross references'', from the Cross Reference Source drop-down menu. Select ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) click on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
##* Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
##*Take a screenshot of this window (on a PC, simultaneously press the <code>Alt</code> and <code>PrintScreen</code> buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.
## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
# '''Analyzing and Interpreting STEM Results'''
## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following:
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##* '''''How many genes belong to this profile?'''''
##* '''''How many genes were expected to belong to this profile?'''''
##* '''''What is the p value for the enrichment of genes in this profile?''''' Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
##* Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
##** Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor that was deleted from your strain?'''''
##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].

==Powerpoint and Zip==
[[Media:StemGraphResults.pptx|dGLN3 Stem Graph Result Powerpoint]]
[[Media:DGLN3_STEM.zip|DGLN3 Zip File]]

Zvanysse Week 10

2017-11-03T20:24:50Z

Zvanysse: uploading powerpoint

==Powerpoint==
[[Media:StemGraphResults.pptx|dGLN3 Stem Graph Result Powerpoint]]

File:StemGraphResults.pptx

2017-11-03T20:21:47Z

Zvanysse:

Zvanysse Week 9

2017-10-31T01:30:28Z

Zvanysse: adding how I got to curl

==URL==
http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?content-type=application/json;expand=1
 
curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?' -H 'Content-type:application/json'
*Note: an explanation is provided in the Electronic Workbook.

==Electronic workbook==
First, we downloaded three files with different file extensions: .xlsx, .graphml, and .sif. The three files are:

#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.graphml
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.sif
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx

Note how these are the same files as my homework partner, Antonia Porras.
===Test 1===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 2===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 3===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 4===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test3_biodb_zv.PNG | 800x800px]]
===Test 5===
First, we went to GRNsight and imported the Sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test4_biodb_zv.PNG | 800x800px]]
===Test 6===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test5_biodb_zv.PNG | 800x800px]]
===Test 7===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 8===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 9===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 10===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 11===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 12===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 13===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 14===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 15===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 16===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 17===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 18===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

==URL Explanation==
First, I decided to go from the middle out. At first, I noticed that I could just change the ID name in this URL: "http://rest.ensembl.org/lookup/id/YPL084W?content-type=application/json;expand=1" however this does not get from the actual name "BRO1" to the relevant information. So I browsed the API dictionary knowing that I had to use both "BRO1" and "saccharomyces_cerevisiae" in the URL. I came across a lookup guide that takes in the Gene name and related species and spews out the information on that gene. This is how I arrived at this part of the URL: "http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?" The next part was figuring out the content-type=application/json part. This is basically just a necessary logistical part that lets the service know that the user wants a json format. "expand=1" basically expands the information into more data. I wasn't sure if it was necessary, but the data was relevant so I decided to go forth and add it in.
#type in http://rest.ensembl.org/lookup/symbol/
#Type in the relevant species followed by a "/" Example: "saccharomyces_cerevisiae/"
#Type in the desired gene symbol followed by a question mark, i.e. "BRO1?"
#For json users, type in content-type=application/json
#If you would like to know more data, place a semi-colon after "json" and type "expand=1"

Here is the URL: 
http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?content-type=application/json;expand=1 

Alternatively, we can use the curl method to retrieve the data, it is pretty much the same except that the syntax is a little different. First, add "curl" to the beginning of it and separate the URL before the "content-type." instead, type " -H " and then type the "content-type=application/json;" Not that there is not a need for the expand=1;
 
Here is the curl function: 
curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?' -H 'Content-type:application/json'
==Acknowledgments==
*I worked with Antonio Porras to complete the test cases.
*I consulted with Arash on clarifying what the URL question was asking
*'''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]]) 00:33, 30 October 2017 (PDT)

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

Zvanysse Week 9

2017-10-31T01:20:52Z

Zvanysse: /* URL */

==URL==
http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?content-type=application/json;expand=1
 
curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?' -H 'Content-type:application/json'
*Note: an explanation is provided in the Electronic Workbook.

==Electronic workbook==
First, we downloaded three files with different file extensions: .xlsx, .graphml, and .sif. The three files are:

#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.graphml
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.sif
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx

Note how these are the same files as my homework partner, Antonia Porras.
===Test 1===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 2===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 3===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 4===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test3_biodb_zv.PNG | 800x800px]]
===Test 5===
First, we went to GRNsight and imported the Sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test4_biodb_zv.PNG | 800x800px]]
===Test 6===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test5_biodb_zv.PNG | 800x800px]]
===Test 7===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 8===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 9===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 10===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 11===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 12===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 13===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 14===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 15===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 16===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 17===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 18===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

==URL Explanation==
First, I decided to go from the middle out. At first, I noticed that I could just change the ID name in this URL: "http://rest.ensembl.org/lookup/id/YPL084W?content-type=application/json;expand=1" however this does not get from the actual name "BRO1" to the relevant information. So I browsed the API dictionary knowing that I had to use both "BRO1" and "saccharomyces_cerevisiae" in the URL. I came across a lookup guide that takes in the Gene name and related species and spews out the information on that gene. This is how I arrived at this part of the URL: "http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?" The next part was figuring out the content-type=application/json part. This is basically just a necessary logistical part that lets the service know that the user wants a json format. "expand=1" basically expands the information into more data. I wasn't sure if it was necessary, but the data was relevant so I decided to go forth and add it in.
#type in http://rest.ensembl.org/lookup/symbol/
#Type in the relevant species followed by a "/" Example: "saccharomyces_cerevisiae/"
#Type in the desired gene symbol followed by a question mark, i.e. "BRO1?"
#For json users, type in content-type=application/json
#If you would like to know more data, place a semi-colon after "json" and type "expand=1"

==Acknowledgments==
*I worked with Antonio Porras to complete the test cases.
*I consulted with Arash on clarifying what the URL question was asking
*'''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]]) 00:33, 30 October 2017 (PDT)

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

Zvanysse Week 9

2017-10-30T20:34:40Z

Zvanysse: fixed a typo

==URL==
http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?content-type=application/json;expand=1
*Note: an explanation is provided in the Electronic Workbook.
==Electronic workbook==
First, we downloaded three files with different file extensions: .xlsx, .graphml, and .sif. The three files are:

#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.graphml
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.sif
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx

Note how these are the same files as my homework partner, Antonia Porras.
===Test 1===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 2===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 3===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 4===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test3_biodb_zv.PNG | 800x800px]]
===Test 5===
First, we went to GRNsight and imported the Sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test4_biodb_zv.PNG | 800x800px]]
===Test 6===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test5_biodb_zv.PNG | 800x800px]]
===Test 7===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 8===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 9===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 10===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 11===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 12===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 13===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 14===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 15===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 16===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 17===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 18===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

==URL Explanation==
First, I decided to go from the middle out. At first, I noticed that I could just change the ID name in this URL: "http://rest.ensembl.org/lookup/id/YPL084W?content-type=application/json;expand=1" however this does not get from the actual name "BRO1" to the relevant information. So I browsed the API dictionary knowing that I had to use both "BRO1" and "saccharomyces_cerevisiae" in the URL. I came across a lookup guide that takes in the Gene name and related species and spews out the information on that gene. This is how I arrived at this part of the URL: "http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?" The next part was figuring out the content-type=application/json part. This is basically just a necessary logistical part that lets the service know that the user wants a json format. "expand=1" basically expands the information into more data. I wasn't sure if it was necessary, but the data was relevant so I decided to go forth and add it in.
#type in http://rest.ensembl.org/lookup/symbol/
#Type in the relevant species followed by a "/" Example: "saccharomyces_cerevisiae/"
#Type in the desired gene symbol followed by a question mark, i.e. "BRO1?"
#For json users, type in content-type=application/json
#If you would like to know more data, place a semi-colon after "json" and type "expand=1"

==Acknowledgments==
*I worked with Antonio Porras to complete the test cases.
*I consulted with Arash on clarifying what the URL question was asking
*'''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]]) 00:33, 30 October 2017 (PDT)

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

Zvanysse Week 9

2017-10-30T07:33:45Z

Zvanysse: Uploaded link

==URL==
http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?content-type=application/json;expand=1
*Note: an explanation is provided in the Electronic Workbook.
==Electronic workbook==
First, we downloaded three files with different file extensions: .xlsx, .graphml, and .sif. The three files are:

#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.graphml
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.sif
#https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx

Note how these are the same files as my homework partner, Antonia Porras.
===Test 1===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 2===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 3===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be selected. We did this by dragging the nodes trying to bring them outside of the view port. The test '''PASSED''' with no errors.
===Test 4===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test3_biodb_zv.PNG | 800x800px]]
===Test 5===
First, we went to GRNsight and imported the Sif file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test4_biodb_zv.PNG | 800x800px]]
===Test 6===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if it were to be unchecked. We did this by dragging the nodes trying to bring them outside of the view port. The test '''FAILED''' with the following errors: Unable to move nodes outside of the box on the right, top, and left, but was able to on the bottom. Below is an example image: [[File:Test5_biodb_zv.PNG | 800x800px]]
===Test 7===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 8===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 9===
First, we went to GRNsight and imported the GraphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 10===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 11===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 12===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 13===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 14===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 15===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was selected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors.
===Test 16===
First, we went to GRNsight and opened the excel file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 17===
First, we went to GRNsight and imported the sif file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)
===Test 18===
First, we went to GRNsight and imported the graphML file. We checked to see if any of the nodes would go outside of the view port window if we decreased zoom, when the view port window was deselected. We did this by dragging the zoom slider. The test '''PASSED''' with no errors accounting for the understanding that the actual view port deselection is buggy in itself (Noted in tests 4-6)

==URL Explanation==
First, I decided to go from the middle out. At first, I noticed that I could just change the ID name in this URL: "http://rest.ensembl.org/lookup/id/YPL084W?content-type=application/json;expand=1" however this does not get from the actual name "BRO1" to the relevant information. So I browsed the API dictionary knowing that I had to use both "BRO1" and "saccharomyces_cerevisiae" in the URL. I came across a lookup guide that takes in the Gene name and related species and spews out the information on that gene. This is how I arrived at this part of the URL: "http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/BRO1?" The next part was figuring out the content-type=application/json part. This is basically just a necessary logistical part that lets the service know that the user wants a son format. "expand=1" basically expands the information into more data. I wasn't sure if it was necessary, but the data was relevant so I decided to go forth and add it in.
#type in http://rest.ensembl.org/lookup/symbol/
#Type in the relevant species followed by a "/" Example: "saccharomyces_cerevisiae/"
#Type in the desired gene symbol followed by a question mark, i.e. "BRO1?"
#For json users, type in content-type=application/json
#If you would like to know more data, place a semi-colon after "json" and type "expand=1"

==Acknowledgments==
*I worked with Antonio Porras to complete the test cases.
*I consulted with Arash on clarifying what the URL question was asking
*'''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]]) 00:33, 30 October 2017 (PDT)

==Links==
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