[Bioperl-l] GSoC 2011

Dave Messina David.Messina at sbc.su.se
Tue Mar 29 05:11:26 EDT 2011

Hi Fei,

Glad to hear you're interested in working on BioPerl!

Just to throw in my two cents, I think it would be great to have a RAxML
wrapper in BioPerl. Although actually any of the projects you mentioned
sound like they're about the right size for a summer project.

I'm not directly involved with GSoC, so I think if you haven't already you
should take a look at our GsOC page here


and get in touch with Rob Buels, our coordinator (rmb32 at cornell.edu)


On Tue, Mar 22, 2011 at 20:14, Fei Hu <hufeiyc at gmail.com> wrote:

> Hi, All.
> My name is Fei Hu from U. of South Carolina. I am currently a second-year
> Ph.D student in computer science focusing on gene order and sequence(DNA &
> AA) phylogeny as well as whole genome alignment. I am instreseted in
> joining
> bioperl project of GSoC 2011. I have two ideas that would like to share.
> My first idea is to extend the bioperl so that it can process and analysis
> gene order data using published package such as MGR, GRAPPA and distance
> estimator. This is a relatively new type of data and many great researchers
> have contributed to this type of phylogeny reconstruction (Dr. Pavel
> Penzer,
> Dr. Bernard Moret and Dr. David Sankoff).
> Secondly as maximum likelihood becomes more and more popular, especially
> RAxML has been widely recognized and used(over 1000 citations). I think
> it's
> time to integrate that as well as GARLI into the Bio::Tools. I extensively
> used and explored RAxML in my last publication on gene order phylogeny.
> Those are just my preliminary thoughts, not even a plan and any suggestion
> is greatly appreciated!!! I use perl on daily bases for data processing and
> composing testing scripts, but not much OOP involved.
> PS: Rest api for CIPRES is no longer available. So this following task
> can't
> be finished right now:
> Development of a
> Bio::Tools::Run::RemoteBlast<
> http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
> interface to CIPRES remote analyses; for more see this
> thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
> .
> And Thank you all.
> Best
> Fei
> --
> *Fei Hu
> Bioinformatics Lab
> 3D-11 Swearingen Building
> U of South Carolina
> Tel: 803-397-5240*
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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