Simonwro120 Week 15

Electronic Notebook

JASPAR the Friendly Ghost Final Group Presentation | December 11, 2017

Tuesday (12/5/17)

• Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application.
  • Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork.
  • Became familiar with the GRNsight code for future implementation.

Thursday(12/7/17)

• Worked with Eddie B. and Dr. Dionisio on the API requests. Attempting to create a solution to the CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database.
  • Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller.

Deliverable Checklist

1. Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
   • Project Manager (Quinn) will ensure that all the deliverables are organized and delivered properly and on time.
2. Group Report (.doc, .docx or .pdf file)
   • Outline
   1. Abstract
      • Primarily Quinn - Additional input/information from the entire group as well
   2. Intro
      • Primarily Quinn - Additional input/information from the entire group to facilitate flow
   3. Materials and Methods
      • Primarily Antonio, Eddie, and Simon
   4. Results
      • Primarily Antonio, Eddie, and Simon
   5. Discussion
      • All members
   6. Conclusions
      • All members
   7. Acknowledgements
      • All members
   8. References
      • All members
3. Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
4. Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
5. Code (GitHub pull request)
   • Each team should coordinate in performing a final integration and integration testing iteration (see Coder milestone for details) which the Interaction and Integration team then submits to the original GRNsight GitHub repository as a single, unified pull request from the class project’s fork
6. Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
7. Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
8. PowerPoint of screenshots of stem results (.pptx)
9. Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
10. YEASTRACT "rank by TF" results (.xlsx)
11. GRNmap input workbook (with network adjacency matrix, .xlsx)
12. GRNmap output workbook (.xlsx)
13. Electronic notebook corresponding to these the microarray results files (Week 8, Week 10, and Weeks 11-15) support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.

Acknowledgements

• I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
• Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
• I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
• While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

1. LMU BioDB 2017. (2017). Retrieved December 7, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
2. LMU BioDB 2017. (2017). Retrieved December 7, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3
3. API Overview. (2017). Retrieved December 5, 2017, from http://jaspar.genereg.net/api/overview#cors-requests
4. JASPAR RESTful API. (2017). Retrieved December 5, 2017, from http://jaspar.genereg.net/api/