QLanners Week 15

Deliverables

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

Media:JASPAR_Final_Paper.pdf | December 15, 2017

Electronic Notebook

On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

1. Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
   • Quinn will take care of ensuring all deliverables are organized and delivered properly.
2. Group Report (.doc, .docx or .pdf file)
   • The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section
   1. Abstract
      • Primarily Quinn - with input from everyone
   2. Intro
      • Primarily Quinn
   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)
   • Each member will complete this task individually
4. Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
   • All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
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
   • Eddie and Simon
6. Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
   • Eddie and Simon (Quinn help if needed)
7. Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
   • Antonio
8. PowerPoint of screenshots of stem results (.pptx)
   • Antonio
9. Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
   • Antonio
10. YEASTRACT "rank by TF" results (.xlsx)
    • Antonio
11. GRNmap input workbook (with network adjacency matrix, .xlsx)
    • Antonio
12. GRNmap output workbook (.xlsx)
    • Antonio
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.
    • Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report:

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used Lucid Chart to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, our group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my statement of work page and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minute corrections).

Fields unable to retrieve. (This list is incomplete, as I tried to connect with Eddie and John through text on multiple occasions, but never got any responses):

• Similar Proteins (UniProt)

Acknowledgements

• All of the JASPAR the Friendly Ghost team members for the collaborative effort.
• Eddie A and John Lopez for providing me information on what (if any) fields were unretrievable from certain databases.
• Dr. Dahlquist and Dr. Dondi for their help and guidance throughout the semester.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Qlanners (talk) 11:11, 14 December 2017 (PST)

References

LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com

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