JASPAR the Friendly Ghost

Deliverables

Eddie and Simon Chapter 6 Presentation | November 14, 2017
GitHub fork
GitHub jaspar-api branch

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 and develop candidate gene reg network	1	2
3	4	5 C: Retrieval code for API DA:Model gene reg network	6	7 C: Review and Test Code PM: Review and Test code DA: Visualize results	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

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.
Individual Journal Page: simonwro120 Week 11
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.

• What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.
• What didn't work? Nothing specific prevented us from working efficiently.
• 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) 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 t 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. Qlanners (talk) 15:12, 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

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)

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)

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. 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
7. 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.
8. 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.
9. 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/
10. Hybridization. (2008). Biology-Online. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
11. 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.
12. 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.
13. 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.
14. Oligonucleotide. (2014). News Medical Life Sciences. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
15. Polypropylene. (n.d.). Dictionary.com. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
16. Putative. (2014). Biology-Online. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
17. Transcriptome. (n.d.). Nature. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
18. 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
19. 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:

• Week 11: Quinn Lanners | Antonio Porras | Edward Bachoura | Simon Wroblewski
  
• Week 12: Quinn Lanners | Antonio Porras | Edward Bachoura | Simon Wroblewski
  
• Week 13: Thanksgiving Break
  
• Week 14: Quinn Lanners | Antonio Porras | Edward Bachoura | Simon Wroblewski
  
• Week 15: Quinn Lanners | Antonio Porras | Edward Bachoura | Simon Wroblewski
  

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