[Bioperl-l] Suggestions for MATLAB-Bioperl Interface

[Catherine Letondal]

On Fri, Oct 10, 2003 at 11:29:35AM -0400, Brian Madsen wrote:
> 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.
> 

This is probably at a research stage only, but I came accross
"Lightweight Languages" which are (as far as I have understood) an
attempt to address complex programming situations such as this
one. Communication with differing subsystems is addresed also, but the
idea goes much further.

http://www.mail-archive.com/perl6-internals@perl.org/msg17089.html

A more detailed description of the field is provided here:
http://www.usenix.org/publications/library/proceedings/dsl97/full_papers/spinellis/spinellis_html/spinellis.html


-- 
Catherine Letondal -- Pasteur Institute Computing Center