Simonwro120 Week 15

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Electronic Notebook

Template for Links

List of Assignments

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

List of Journal Entries

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

List of Shared Journals

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

Deliverables

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
  • Near the end of class, Quinn, Antonio, Eddie and myself all exchanged e-mails so that we could all start working on both the powerpoint and paper in a collaborative manner
  • Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller later on that week

Monday (12/11/17)

  • Finalized all the slides for the JASPAR powerpoint presentation, planned roles, speaking order, and general flow
  • Uploaded the powerpoint to our team page, deliverables page, and individual page

Tuesday (12/11/17)

  • Met before class to drill through the presentation a couple times to make sure all things were in check

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)
    • Team members should complete this task individually
  4. Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
    • Separate sections were completed by different members of the group initially
    • Merged separated sections together to create a coherent and informative powerpoint presentation
    • Practiced verbal presentation until it was executed smoothly
  5. Code (GitHub pull request)
    • As stated previously, Blair forked from Dondi, and the rest of the class coned that forked repository.
  6. Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
    • Coders should create this explanatory file, project manager may have some input as well
  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.
    • Deliverables 7 - 13 came from our Data Analyst's (Antonio) hard work

Final Paper/Group Report

Media:JASPAR Final Paper.pdf

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.

Simonwro120 (talk)

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/
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