[Biojava-l] Framework VI Expression of Interest

[David Huen]

On Fri, 5 Apr 2002, Jean-Marie Buerstedde wrote:

> 
> I think there is ample opportunity to obtain funding for a biojava 
> initiative and it seems to be advantageous to get as many as possible 
> centers and people involved. One idea among others could be to propose 
> JAVA and especially J2EE as the platform of choice for bioinformatic 
> programing and the distribution and analysis of genomic data over the 
> internet. I would also favor to make the whole project open source, but 
> if needed one could think about compromises.
> 

Just my $0.02 worth (where is the Euro key on this keyboard?):-

Some care needs to be taken here to avoid language wars.  If the promotion
of Java is seen as a threat to other languages, it can only antagonise
some who may have a role in assessing the proposal.

Re: the open source issue.  We have a number of significant contributions
to BioJava from commercial outfits  like CAT (Simon Brocklehurst, output
parsers) and AgResearch NZ (Mark Schrieber) who have participated on the
basis of the current licensing and I am apprehensive of licensing changes
that may prejudice continued participation of parties like these.

I wonder whether if an attempt were made, whether it would be better
pursued on a language-neutral basis as with the OBF affiliates with
parties contributing solutions, some (hopefully many) of which are
BioJava-based. As the network is the glue here, the language of
implementation is not the critical factor.  BioJava may end up with a
smaller cut of what might be a bigger pie with better chances of getting
funded than if it did as a language specific proposal.  I think a united
presentation by OBF affiliates would look a lot more politically credible.

Given the ongoing DAS efforts in this very area and the improvements in
genomic data distribution already accruing from these open efforts, I hope
a proposal will not attempt to invent yet another protocol for this
purpose rather than building on and extending the existing efforts.

Anyway, just my thoughts...

Best wishes,
David Huen