[Biojava-dev] Participation

[David Huen]

On Mon, 1 Dec 2003, Dennis, Glynn (NIH/NIAID) wrote:

> I would like to discuss with you how we might be able to contribute to
> BioJava.  We develop applications (in java) that facilitate the biological
> interpretation of functional genomic data sets, such as those derived from
> microarrays and proteomics.  We have several parsers and analysis modules
> that we would consider including in BioJava as part of a larger goal of open
> source code for dealing with functional genomic data analysis.
> 
> Please let me know your level of interest and advise towards a next step.
> 
I would be happy to discuss the inclusion of the code you have developed.
I speak for myself (of course!) but I think the following statemets
probably reflect the views of most developers here.

As you probably already know, BioJava is LGPL-licenced - this was chosen
to avoid "virally" infecting applications that users of the code might
wish to develop while maintaining copyleft on the library itself.  I do
not envisage LGPL restricting your continued use and even
commercialisation of your own code since you are still the original
copyright holders.

The sequence model in BioJava may seem strange at first sight but it does
have the merit of being extendable to arbitrary sequence types and also
being strongly typed.  If your code has references to sequences and
locations on sequences, those parts may need some reworking to get good
interoperability with the rest of the code.

We could do with considerable strengthening in the functional genomics
area and any assistance and gifts of code will be warmly welcomed.

Regards,
David Huen