Difference between revisions of "JASPAR the Friendly Ghost"

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(→‎Antonio's Executive Summary: "found in deliverables)
(→‎Antonio's Reflection: reflection)
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====Antonio's Reflection====
 
====Antonio's Reflection====
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# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
 +
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
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# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.
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[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)
  
 
====Eddie's Reflection====
 
====Eddie's Reflection====

Revision as of 02:36, 4 December 2017

Deliverables

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)

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
  6. Screenshot of GRNsight Regulatory Network: Media:AP Regulation Matrix profile22 GRNsight Network.PNG

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

Simon's Executive Summary

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

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

Simon's Reflection

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

Acknowledgements

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.
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  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.

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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