This summer I’ll be working with the BioRuby development community adding gene duplication inference functionality to the code base. I’m very excited about being selected to complete the project.

Coding doesn’t start until the end of May, giving me plenty of time to a) finish up my semester and b) get set up and familiar with BioRuby before I dive into the implementation.

Tasks for the community bonding period:

  1. *COMPLETED* Subscribe to BioRuby mailing list and introduce myself and the project.
  2. *COMPLETED* Familiarize myself with the Git distributed version control system, as well as GitHub.
  3. *COMPLETED* Set up the BioRuby code base. Here’s my repository.
  4. *COMPLETED* Install the Archaeopteryx tree viewer.
  5. *COMPLETED* Obtain the forester Java source which contains an implementation of the SDI algorithms, instructions for this here, also here.
  6. *COMPLETED* Set up a blog… for example
  7. *COMPLETED* Reading, reading, reading…Obtain theseĀ papers.
  8. *COMPLETED* Also, obtain copies of:

Finally, update and revise project plan.

It’s going to be a busy month, and a busy summer.