BIOL388/S19:Week 5

The finished version of the Week 4/Week 5 assignment is due Thursday, February 21 at midnight PST. (Wednesday night/Thursday morning) The full write-up of the assignment is on the Week 4 page. You should not have a separate Week 5 individual journal page, just update your Week 4 assignment.

Summary of what you need to turn in for the individual Weeks 4 and 5 assignments

You will continue working on your Week 4 individual journal page for the Week 5 assignment as well. The two assignments will be graded together after the Week 5 due date for 20 points, instead of individually for 10 points each.

By the Week 4 deadline, submit:

1. Your individual journal page should have an electronic lab notebook recording your work for this week. This includes the purpose, detailed methods, your results, the answers to any questions posed in the protocol above, a scientific conclusion, and the acknowledgments and references sections. You are responsible for completing the procedure up to the designated stopping point.
2. Upload your updated Excel spreadsheet to Box that has today's calculations in it. Use the same filename as before so that the download link that you already provided to Drs. Dahlquist and Fitzpatrick will still work.
3. Create, upload to OpenWetWare, and link to a PowerPoint presentation that contains the p value table. You will need to zip it because OWW does not accept .ppt or .pptx as a file format anymore.

By the Week 5 deadline, submit:

1. Continuation of the individual journal page for Week 4 with your electronic lab notebook recording your work for the last two weeks. This includes the purpose, detailed methods, your results, the answers to any questions posed in the protocol above, a scientific conclusion, and the acknowledgments and references sections. You will add to what you submitted to the interim deadline on Week 4. Don't forget your paragraph which is a biological interpretation of your stem results.
2. Add the screenshots of your stem results to the PowerPoint file from last week. Do not change the filename, just upload a newer version of the file. Each slide in the presentation should have a meaningful title that describes the main message of the slide. These slides will form the basis of your research presentation for this project.
3. Zip together all of the tab-delimited text files that you created for and from stem and upload them to Box:
   • the file that was saved from your original spreadsheet that you used to run stem
   • each of the genelist and GOlist files for each of your significant profiles.
4. The shared journal assignment below.

Shared Journal Assignment

The shared journal assignment will be due on the Week 5 deadline, midnight, February 21 (Wednesday night/Thursday morning).

• Store your shared journal entry in the shared Class Journal Week 4 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Link to your journal entry from your user page.
• Link back from the journal entry to your user page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "BIOL388/S19" category to the end of the wiki page (if someone has not already done so).

View

Now that you've done your own microarray data analysis, we will revisit the case "Deception at Duke".

• View the video: The Importance of Reproducible Research in High-Throughput Biology: Case Studies in Forensic Bioinformatics.
• View the slides from DataONE on data entry and manipulation.
• Optional: for more information on the Duke saga, see the web site put together by Baggerly and Coombes here.

Reflection

1. What were the main issues with the data and analysis identified by Baggerly and Coombs? What best practices enumerated by DataONE were violated? Which of these did Dr. Baggerly claim were common issues?
2. What recommendations does Dr. Baggerly recommend for reproducible research? How do these correspond to what DataONE recommends?
3. Do you have any further reaction to this case after viewing Dr. Baggerly's talk?
4. Go back to the methods section of the paper you presented for journal club. Do you think there is sufficient information there to reproduce their data analysis? Why or why not?