Biomedical Data Design

Biomedical Data Design

Overall goals and structure

Overall goals and structure

The goal of the remainder of the course is to either

  • write a manuscript detailing the work you have already done
  • continue to make PRs into widely-used software packages

If you feel your goals/desires don’t fall under either category, please talk to us so we can see if something else would be feasible.

Sprint 1

Now - March 13

Sprint 2

March 23 - Finals

“Real” PRs

Everyone should have made a PR into a “real” (not our fork) repo by the end of Sprint 1. This means that while the PR may not be merged by those developers right away, it should at least be at a point where TAs/Jovo believe that the code is useful, correct, well documented and coherently written.

Weekly class schedule

Monday, Kavli rooms

The following teams should attend:

  • Tealeaf
  • Forbidden Forest
  • Mouselit

TAs/Jovo will meet with each team individually. On the day you present you should have 1-2 slides based on the slide guidelines below

Wednesday, Kavli rooms

The following teams should attend:

  • Graphs
  • Multiview
  • NDMG

TAs/Jovo will meet with each team individually. On the day you present you should have 1-2 slides based on the slide guidelines below

Friday, Bloomberg

Everyone should attend

Jovo and TAs will do lectures and short tutorials, possibly leaving time to meet with us as well

Submit feedback form by Monday morning

Class guidelines

Slides

General rules for class presentations:

  • One slide
    • Title describes the main takehome message from the figure/results presented on the slide
    • One figure clearly summarizing one main result from this week that this person accomplished
    • Very little text otherwise on the slide
    • Code used to generate the figure linked on the slide or in comments of the slide deck
    • Link to the issue that this result is related to in the appropriate repo
  • One minute of presentation, to leave time for discussion with us

Pull requests

  • Prior to having a PR reviewed by TAs, we will be doing partner code reviews.
    • Work out amongst your team members (or others in the class if you prefer) who will be reviewing your PRs.
    • Everyone in the class should be doing reviews and having their code reviewed.
  • We will have a Google form to request a TA review (and show that your PR was first peer reviewed).
  • Re-reviews can also be requested through this form after verifying that you addressed all of the previous comments.
  • Grades will be based on whether you addressed all previous comments from both your peers and the TAs. Addressing means that you fixed the thing, tried to fix the thing with evidence of why/how you are stuck, or demonstrate adequately why the thing does not need to be fixed.

Office hours

  • This semester we will try having open office hours as opposed to regular group meetings
  • Office hour times:
    • (pending)