[Bioperl-l] a project idea

[Juha Muilu]

Jason Stajich wrote:
> 
> For those of you new who wanted some ideas of how to help out on the
> bioperl project, here is one I was mulling over last night.
> 
--- CUT--- 
> I'd like to suggest the following.  Someone could design an interface
> Bio::Tools::RunI which all these implementations can implement - something
> like a bare minimum - parameters(), run(), output()  and handle checking
> for executable in the path or specified dirs.
> 
> We may want to steal/learn from EnsEMBL pipeline code and/or the OMG specs
> for running analysis through CORBA.
> 

That is interesting! One implementation "plugin" can be BSA/CORBA client, which
gives access to the AppLab analysis engine. 

Martin is currently working with a ORBit bridge. So the OBV issue is not a
problem. 



> Additionally new wrappers to run such applications as
> hmmer,genscan,mzef,sim4,exonerate,fasta,genewise could be written.  Right
> now we are bounded by the need to have the applications' output parsed
> into bioperl objects - this would prevent exonerate or fasta runnables
> from being done right away, but sim4, genscan, and mzef would be a piece
> of cake I suspect.
> 
> Attachment to EMBOSS apps would also be an excellent next step.

EMBOSS is currently working under the AppLab. 

> 
> Once we have RunI objects we can build a RunFactory.
> 
> So in summary - we'd need someone to come up with a specification for how
> to design new Run modules cleanly with an interface and reimplement the
> existing ones to comply to the interface.  Then new modules could be
> rolled out for common apps that people use.  Phrap/RepeatMasker for those
> in the sequencing end would be welcomed as well.
> 
> Anyone interested enough to give it a go, or at least start some wiki
> documentation so we can start collaborating?
> 
> -jason
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center
> http://www.chg.duke.edu/
> 
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