[Biojava-dev] Biojava and biomanycores

[forumjspro at gmail.com]

Dear all,

I'm one of the people who is trying to develop the biomanycores  
project (www.biomanycores.org) which aims to give access to efficient  
parallel algorithms developed for GPUs to bioinformaticians.

To reach this goal we want to provide interfaces to those algorithms  
through Bio* frameworks. People will have to change only some lines in  
their Bio* code to use more efficient tools. In order to realize such  
interfaces, it is necessary to launch the command line tool and to  
retrieve results. I didn't see in the BioJava API a class enabling to  
do such a thing although a mechanism seems to exist in BioPython or  
BioPerl.

I would like to know if I miss something in the API and, if it is not  
the case, what could be the best way to launch external programs to  
stay in the spirit of BioJava. For the moment, I use the trilead  
package to launch commands on distant computers and the Runtime class  
in the standard API to launch local commands. But may be it is  
completely irrelevant to add such functionalities to BioJava.

Please let me know what do you think about it.

Best regards

Jean-Stephane

Jean-Stephane Varre
http://www.lifl.fr/~varre
http://www.lifl.fr/SEQUOIA
http://bioinfo.lifl.fr