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Gmane
From: Leon Timmermans <l.m.timmermans <at> students.uu.nl>
Subject: Re: small project
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 14th May 2012 12:38:42 UTC (over 4 years ago)
On Fri, May 11, 2012 at 9:07 PM, Jason Stajich <[email protected]>
wrote:
> HMMER folks have contributed a module to BioJava to simplify submission
of a protein sequence to the HMMER RESTful API
> http://xfam.wordpress.com/2012/05/09/pdb-pfam-mapping/
> http://hmmer.janelia.org/help/api
>
>
> Perhaps a BioPerl similar module that wraps up the existing code to
submit Bio::Seq objects similar to other Bio::DB:: or probably better to do
Bio::Tools interfaces for interaction with remote webservices. The code to
add this to bioperl is basically already written - the question would be if
you wanted to populate a Bio::Search object with the XML results (Writing a
parser for the XML)
>
> http://hmmer.janelia.org/help/api#sending
>
> Jason

I rather like the Spore concept for this kind of issue. It's a
framework for RESTful webservices that only requires you to write a
description of a webservice (often in json or yaml form) and it will
then generate the code to interact with it from that. A major
advantage is that it's implemented for a range of programming
languages (currently Perl, Python, Ruby, Lua, Clojure, Javascript).
Thinking about this, a wider Bio-Spore project may be a good idea.

Leon
 
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