Difference between revisions of "JASPAR the Friendly Ghost"

Revision as of 23:12, 19 November 2017

The article approved for next week's journal club presentation is Beccera et al. (2003). You can remove this notice when both Quinn and Antonio have read it. — Kdahlquist (talk) 22:54, 14 November 2017 (PST)

Deliverables

Eddie and Simon Chapter 6 Presentation | November 14, 2017

Working Files

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Calendar

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

Simon's Executive Summary

Antonio's Executive Summary

Eddie Bachoura'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

Antonio's Reflection

Eddie's Reflection

Week 12

Quinn's Reflection

Simon's Reflection

Antonios's Reflection

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

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