[Biojava-dev] Feedback on GSoC project proposal

[David Felty]

I made a few modifications to my proposal:
- Dropped the databases section
- Added some extreme programming ideas: frequent testing and mentor
checks, early development of a FASTA implementation
- Compiled a list of existing file parsers
- Added additional "new parsers"

> I'd prefer you to follow extreme programming
> approach rather than having a long planning stage.
The reason I have the long planning stage in there is because those
are the weeks when I'm in school, so I won't have as much time to
dedicate to the project. I did, however, put in the the development of
a FASTA parser, because I think I can handle that, even alongside
schoolwork.

While I was looking through the API, I found a couple of classes I was
unsure about: APFChainXMLParser and AfpChainWriter. I couldn't find
file formats online that mention APF chain XML, but they do seem to be
related to this: http://fatcat.burnham.org/fatcat/fatcathelp.html
Are these classes I should consider including in my project?

Thanks,
David

On Sun, Apr 1, 2012 at 4:28 PM, P. Troshin <to.petr at gmail.com> wrote:
> Good proposal, thank you! I'd suggest a few changes though. I'd drop
> "Reading from remote databases" section. I do not think that in time
> available you will be able to make significant progress on this topic.
> File parsers are such core functionality for BioJava that I think they
> deserve all your attention. Also, I think you should make a plan that
> is a bit more hands on. I'd prefer you to follow extreme programming
> approach rather than having a long planning stage. So, start from
> developing the simplest parsers e.g. FASTA readers and writers. Once
> you done a complete cycle for one parser it will be much easier to
> plan for other parsers. I did not see HMMER 3 parser in your proposal,
> this is unfortunate as HMMER3 is such a widely used tool now that it
> rival Blast itself! In the end of cause it is for you to decide what
> you'd like to be working on, I can only advise you. All proposals will
> be scored by 10-15 mentors on their own merits.
>
> Regards,
> Peter
>
>
> On 1 April 2012 18:42, David Felty <davfelty at gmail.com> wrote
>> I just submitted my proposal here:
>> http://www.google-melange.com/gsoc/proposal/review/google/gsoc2012/dfelt/2001
>> This is just a first draft, so I realize that I may be missing pieces.
>> If anyone has suggestions on how to improve it, I would very much
>> appreciate your feedback. I am especially interested in which parsers
>> are in high demand, so I can better budget my time.
>>
>> Thanks,
>> David
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