[Biopython-dev] Propsal Draft - Timeline.

[Brad Chapman]

Maximiliano and Reece;
Great to see that the proposal is coming along. I'm cc'ing the
developers mailing lists in case others have thoughts as well.

I'll start by echoing some of Reece's comments:

>    - An overview -- without this, it's hard for readers to know how well you
>    understand the context or why the issue is relevant at all. ~5 sentences
>    should suffice. Please take a stab at it and I'll help.

Yes, definitely. This is an application not to Reece, who knows
about the project, but to the general developer community. You need
to justify why this project is important and what you hope to
accomplish. Generally you need to argue for why Google should fund
this project over other equally deserving projects.

>    - Consider adding a short "about me" section.

The reviewers will need detailed information about your background
to assess your ability to be successful. You should add work you've
done previously, especially related to Python. Ideally you will have
links to some open source work you've done so reviewers can assess
your programming experience.

> I'm also cc'ing Brad who may have more input.

The proposal timeline needs to be much more detailed. What it should
look like is a week by week breakdown of what you hope to
accomplish. This will be used by you and your mentors to help track
progress and stay on track. These are the weekly milestones you
mention in your proposal.

Some specific suggestions:

- All non-coding tasks (setting up version control) should be put in
  your timeline prior to the start of the coding period.

- Your weekly goals need to be very specific. For instance 'Design
  the library API' does not tell a reviewer any details about what
  you hope to accomplish. You should have a general idea of what you
  plan to design now, and then be listing these in your plan.

Hope this helps with getting everything finalized before tomorrow,
Brad

> > *Abstract:*
> > *I am still working on it.*
> >
> > *Proposal Timeline:*
> >
> > *Before April 25:*
> >
> >    - To familiarize myself with BioPython.
> >    - Experiment with PLY (Python Lex-Yacc) and Pyparsing.
> >    - Review some basic biology concepts: genomes, transcripts, proteins,
> >    genomic variation, and others suggested by my mentor.
> >    - To familiarize myself with HGVS nomenclature, and experiment using
> >    Mutalyzer 2.0
> >
> >
> > *April 27 - May 24 (Before the official coding time):*
> >
> >    - Define the subset of the HGVS to be represented.
> >    - Identify variation types to be represented (SNV, CNV, repeats,
> >    inversions, etc).
> >    - Design a formal grammar that fully represents the subset of the HGVS
> >    chosen before.
> >    - Define a set of semantic validations for the represented variations.
> >    - Write a short document explaining how to properly extend the formal
> >    grammar defined before.
> >
> >
> > *May 25 - July 12 (Official coding period starts):*
> >
> >    - Set up a control version system and a bug tracker.
> >    - Define weekly milestones.
> >    - Design the library API.
> >    - Develop an abstract variant class and subclasses representing
> >    specific cases of them.
> >    - Design and implement a parser for the formal grammar defined before.
> >    - Test the code written up to now.
> >
> >
> > *July 15: Midterm evaluation*
> >
> > *July 17 – August 16:*
> >
> >    - Work on semantic validations defined before.
> >    - Full testing of the whole library.
> >    - Integration of the library to BioPython.
> >    - Documentation of the whole library.
> >    - Implementation of a syntax checker as an example of the use of the
> >    library. Make it freely availably on the Internet.