[Biopython-dev] GSoC Student Applicant

Brad Chapman chapmanb at 50mail.com
Sun Apr 1 19:28:32 UTC 2012


> Thank you for the comments and suggestions. I've added a little bit
> more details to my personal profile and put it up front. My project
> details have also been broken down into single weeks. And I've edited
> the commenting permission.

Thanks for the updates, this is coming along well. My most general
suggestion is to spend more time expanding the week-by-week
timeline. As an example, take this weekly goal:

* Write iterator and random-access parser for EMBOSS water

It would be great to see more specific plans for what exactly you
deliver and implement during the week. Something like:

- Write iterator for EMBOSS water, expanding test suite to ensure
  produced AlignIO objects are compatible with previous BLAST and HMMER

- Expand index functionality to handle EMBOSS water format for random
  access. Test edge cases: initial records, final records, empty

- Document 'water' parsing with a use case emphasizing differences from
  BLAST and HMMER searching.

Peter probably has more specific thoughts on the actual content but it's
important to think through things in this manner. This will make it
easier to approach weeks during the summer since you'll already have
tasks broken down, and will also demonstrate you've thought about
potential problems and roadblocks and have solutions to overcome them.

> As for my other obligations, I didn't mean to give that impression. I
> added a little bite more detail about the project itself, but I'm not
> sure about the time that I should write. I estimate that at most, for
> each week day, I spend 8 hours doing my Master's project in my lab's
> campus. Since the project started, I usually use the remainder of the
> time (~6 hours/day) for my own personal programming projects. I plan
> to use the personal programming time slot for my GSoC instead, if
> accepted. Should I be this thorough in the proposal?

This is exactly my worry. You're proposing working two full time jobs
all summer long. Not to denigrate your work ethic, but 80 hour weeks are
hard and leave you no time for important things like having a life
outside of work. My suggestion would be to see if you can scale back
your Master's commitments for the summer if accepted into GSoC. This
would definitely improve your proposal since reviewers will worry about
the time commitment.

Hope this all helps,

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