[GSoC] GSoC weekly status report No.1

[Marjan Povolni]

Thanks for the tip, that's a great idea!

--
Marjan

On Sun, May 6, 2012 at 5:00 PM, Robert Buels <rbuels at gmail.com> wrote:

> Hi Marjan,
>
> You should probably incorporate into your test suite all of the test gff3
> files in the test data directory of the Perl Bio::GFF3::LowLevel::Parser.
>  It has coverage for some corner cases that are a little bit tricky.
>
> https://github.com/**solgenomics/bio-gff3/tree/**master/t/data<https://github.com/solgenomics/bio-gff3/tree/master/t/data>
>
> Rob
>
>
> On 05/05/2012 09:07 AM, Marjan Povolni wrote:
>
>> Hello all,
>>
>> It might be a little early, but there has been so much going on in the
>> last
>> 10 days since the results of GSoC were published...
>>
>> http://blog.mpthecoder.com/**post/22380853664/gsoc-weekly-**
>> status-report-no-1<http://blog.mpthecoder.com/post/22380853664/gsoc-weekly-status-report-no-1>
>>
>> A short summary:
>>
>> It has been 10 days since the GSoC results were published, and a lot has
>> happened since then. I got to know the other students and mentors in a
>> longish meeting on Google hangout, I got into a discussion with my mentor
>> on IRC in which we didn’t agree about the parallelization strategy for the
>> parser (experiments will show who’s right) and my inbox is full with mails
>> from my mentor and other students, in which we exchanged loads of
>> interesting ideas. Also, I solved a bug in biogems.info website, which
>> was
>> stopping Pjotr from updating the website with new information about
>> biogems.
>>
>> There is now a GitHub repository for my project:
>>
>> https://github.com/mamarjan/**bioruby-hpc-gff3<https://github.com/mamarjan/bioruby-hpc-gff3>
>>
>> The work for the first week of coding is halfway done too.
>>
>> There seems to be huge interest for a GFF3 parser with more features, like
>> indexing, random access and writing output, and also support for linking
>> into trees of features that are not located close to each other in the
>> file. A fast sequential parser could be used to generate indexes, and the
>> lower-level parts can be used to reorder the file for faster future usage.
>> Based on that, I think this project is a good start.
>>
>> *I would like to ask you if you’re using the GFF3/GTF file formats in your
>>
>> research, to send me example files and descriptions of how are your
>> applications using the data. This way I’ll be able to test the parser
>> against your files and optimize it for your applications. Currently I have
>> GFF files from Ensembl and Wormbase, and Pjotr pointed me to the genome
>> browser web application at wormbase.org.*
>>
>> --
>> Marjan
>>
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>>
>>