JASPAR the Friendly Ghost

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GRNsight Gene Page Project Deliverables

JASPAR the Friendly Ghost Final GRNsight Deliverables Page

Working Deliverables

Final Group Presentation | December 11, 2017
Antonio and Quinn Journal Club Presentation | November 21, 2017
Eddie and Simon Chapter 6 Presentation | November 14, 2017
GitHub fork
GitHub api branch (in collaboration with Gene_hAPI team)
Readme.txt | December 15, 2017
Our code for this feature (also hAPI team's code) | December 15, 2017

Working Files

Antonio's Working Files

  1. Gene list for profile 22 of dZAP1 Excel file: Media:AP dZAP1 profile22 genelist.xlsx
  2. YEASTRACT Transcription Factor Data: Media:AP YEASTRACT Transcription Factors.xlsx
  3. YEASTRACT Regulation Matrix Profile: Media:AP Regulation Matrix profile22 dZAP1.xlsx
  4. YEASTRACT Adjacency Matrix: Media:AP Adjacency Matrix profile22 dZAP1.xlsx
  5. YEASTRACT Adjacency Matrix with Network for GRNsight: Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx

Calendar

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

Executive Summaries

Week 11

Quinn's Executive Summary

Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock:

Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301

Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools.
Individual Journal Page: QLanners Week 11
Qlanners (talk) 00:25, 14 November 2017 (PST)

Simon's Executive Summary

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

Antonio's Executive Summary

Created two citations for the bibliography for the following articles:

  1. Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
  2. Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

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

Aporras1 (talk) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: Aporras1 Week 11

Eddie Bachoura's Executive Summary

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

Individual Journal Week 11: Eddie Bachoura Week 11
Ebachour (talk) 23:29, 13 November 2017 (PST)

Week 12

Quinn's Executive Summary

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

Simon's Executive Summary

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

Antonio's Executive Summary

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

Individual journal page: Aporras 1 Week 12

Aporras1 (talk) 22:19, 20 November 2017 (PST)

Eddie Bachoura's Executive Summary

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

Week 14

Quinn's Executive Summary

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

Simon's Executive Summary

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

Antonio's Executive Summary

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

Aporras1 (talk) 18:31, 3 December 2017 (PST)

Eddie's Executive Summary

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

Week 15

Quinn's Executive Summary

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

Simon's Executive Summary

Antonio's Executive Summary

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

Aporras1 (talk) 10:38, 15 December 2017 (PST)

Eddie's Executive Summary

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

Weekly Reflections

Week 11

Quinn's Reflection

  1. What worked?
    • Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
  2. What didn't work?
    • I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
  3. What to improve upon going forward?
    • Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.

Qlanners (talk) 00:25, 14 November 2017 (PST)

Simon's Reflection

  1. What worked?
    • Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
  2. What didn't work?
    • Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
  3. How will to improve upon going forward?
    • Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications.

Simonwro120 (talk) 22:48, 20 November 2017 (PST)

Antonio's Reflection

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

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

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

Aporras1 (talk) 22:06, 20 November 2017 (PST)

Eddie's Reflection

Found in Week 11 summary ^^^

Week 12

Quinn's Reflection

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

Qlanners (talk) 15:12, 20 November 2017 (PST)

Simon's Reflection

  1. What worked?
    • With Eddie's help, we were both able to set up GRNsight on our laptops.
  2. What didn't work?
    • Nothing in specific stopped us from working efficiently.
  3. How will to improve upon going forward?
    • Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections.

Simonwro120 (talk) 22:48, 20 November 2017 (PST)

Antonio's Reflection

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

Aporras1 (talk) 22:12, 20 November 2017 (PST)

Eddie's Reflection

  1. What worked?
    Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
  2. What didn't work?
    Nothing :D

Ebachour (talk) 21:47, 20 November 2017 (PST)

Week 14

Quinn's Reflection

  1. What Worked?
    • This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
  2. What didn't work?
    • I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
  3. What will I do next to fix what didn't work>
    • I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class.

Qlanners (talk) 21:05, 4 December 2017 (PST)

Simon's Reflection

  1. What Worked?
    • Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
  2. What didn't work?
    • There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
  3. What will I do next to fix what didn't work?
    • I hope to be more knowledgeable about these type of things in reference to computer science.

Simonwro120 (talk) 21:57, 4 December 2017 (PST)

Antonio's Reflection

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

Aporras1 (talk) 18:36, 3 December 2017 (PST)

Eddie's Reflection

  1. What worked?
    • We were able to figure out exactly how to extract the info we needed from JASPAR.
  2. What didn't work?
    • We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
  3. How will to improve upon going forward?
    • We decided to merge our two branch which helped with this and kept us on the same page.

Ebachour (talk) 23:25, 4 December 2017 (PST)

Week 15

Quinn's Reflection

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

Qlanners (talk) 21:13, 14 December 2017 (PST)

Simon's Reflection

Antonio's Reflection

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

Eddie's Reflection

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

Ebachour (talk) 13:09, 15 December 2017 (PST)

Acknowledgements

  1. A huge thank you to both Dr. Dahlquist and Dr. Dionisio for taking the time to teach this course and support us, the students, throughout the semester's challenges.
  2. The JASPAR The Friendly Ghost team for working as a cohesive unit.
  3. The Department of Biology at LMU.
  4. The Department of Computer Science at LMU.
  5. The entire class composed of students who we worked alongside throughout the semester.

References

Week 11

  1. LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
  2. Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
  3. Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
  4. Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
  5. 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.
  6. Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
  7. What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
  8. What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
  9. Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
  10. What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
  11. Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
  12. Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

Week 12

  1. LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
  2. Anneal. (n.d.). Genscript. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
  3. Assay.(2005). Biology-Online. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
  4. Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
  5. Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
  6. Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
  7. Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
  8. Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
  9. Cyclins. (n.d.). BioNinja. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
  10. Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
  11. Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
  12. Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
  13. Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
  14. Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
  15. HAW. (2011). Difference Between Haploid and Diploid. Difference Between.com. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
  16. Hybridization. (2008). Biology-Online. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
  17. Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
  18. Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
  19. LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
  20. Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
  21. (n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
  22. (n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
  23. Oligonucleotide. (2014). News Medical Life Sciences. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
  24. Polypropylene. (n.d.). Dictionary.com. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
  25. Putative. (2014). Biology-Online. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
  26. Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
  27. Transcriptome. (n.d.). Nature. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
  28. Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
  29. Young, F.W. (1999). Principle Components. forrest.psych.unc.edu. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
  30. Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

Week 14

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

Week 15

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

Team Links

Course Home Page
JASPAR the Friendly Ghost Team Page
JASPAR the Friendly Ghost Final GRNsight Deliverables Page
JASPAR Database
Team Member's Pages: Quinn Lanners Project Manager/QA | Antonio Porras Data Analyst | Eddie Bachoura Coder | Simon Wroblewski Coder
Instructors: Dr. Dondi | Dr. Dahlquist
Individual Journal Pages:

Class Links

GRNsight Gene Page Project Links
Overview Deliverables Reference Format Guilds Project Manager Quality Assurance Data Analysis Coder
Teams Page Desiigner Lights, Camera, InterACTION! Gene hAPI JASPAR the Friendly Ghost
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