[Bioperl-l] Bioperl in 2005

Paulo Almeida paulo.david at netvisao.pt
Thu Dec 30 06:41:24 EST 2004

I've been wanting to get more involved in BioPerl, but I need to learn 
more about Perl first (namely, the object-oriented parts). I am 
learning about packages and modules (just bought Mastering Perl for 
Bioinformatics!), so it would be great to contribute to BioPerl, as 
that would also help me learn more (which is also one of the good 
things about Open Source).

I have been working on a Phylogenetic Profiler (basically, an automatic 
scan of a number of species for the presence of orthologs of proteins 
of interest, based on Blast E-values), and on a script that computes 
the correlation between two protdist matrices, obtained from the 
protein sequences of a number of species (the optimistic goal is to 
infer protein co-evolution/interaction from good correlations). Could 
something like this be interesting for BioPerl? Either way, I wouldn't 
mind trying your specific suggestions too.


On Dec 29, 2004, at 22:46, Jason Stajich wrote:

> How can you help out?
> (...)
> I can only hope to influence some more folks who might have wanted to 
> contribute but were waiting for the invitation.  Well come on over, 
> we'd love to have you taking part.
>   As for some specifics.
>   - Parsing of Species information out from the ORGANISM lines in 
> SwissProt, GenBank, and EMBL is pretty spotty and could take some 
> work.
>   - Some more parsers for formats that people have asked for - a 
> Spidey parser (NCBI's mRNA -> genomic alignment tool)
>   - Work on the Structure modules for dealing with protein structure 
> data
>   - Integrate new applications into bioperl-run and further cleanup 
> the existing modules so they are more consistent
>   - Volunteer to be the next release master.

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