[Bioperl-l] Suggestions for MATLAB-Bioperl Interface

[Brian Madsen]

I am studying Bioinformatics through the Master's program at
Northeastern and am working as a co-op at MathWorks on their
Bioinformatics Toolbox.

In August, I met a few researchers around Boston to get ideas on the
Toolbox. One of the best suggestions was from a current user, Dr. Vamsi
Mootha at the Whitehead Institute. He was interested in calling Bioperl
apps from MATLAB and calling MATLAB functions from Bioperl. While I
don't yet have a streamlined approach for calling MATLAB from Perl, I
have gone through the installation of Bioperl and tested calling Perl
apps from the toolbox (attached is an html of a demo).

2 questions:
1 - Are there any suggestions on the interface for MATLAB and
Bioperl--any procedures or issues I should research?
2 - What intellectual property issues might be involved? With the base
of Bioperl modules available, I thought it might be a good idea to
include an installation of Bioperl on the Bioinformatics Toolbox CD.

Thanks for any ideas.

-Brian Madsen
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