[Biojava-l] BSA bridge

[Juha Muilu]

Hi

Last year, under the auspices of the Object Management Group (OMG), a
collection of bioinformatics academic and commercial centres discussed,
defined and proposed a set of interfaces (defined in IDL) for
'Biomolecular Sequence Analysis' (BSA). (see http://www.omg.org/lsr/)

As part of the standardisation process, the EBI has written an
implementation of the BSA specification called OpenBSA
(please see http://industry.ebi.ac.uk/openBSA/)

We've also just finished a client-side bridge between OpenBSA and
BioJava
for converting BSA results into BioJava Sequence and SequenceIterator
objects (including Annotations and Features). So, within a Java program,
you may connect to a BSA server and run an analysis, then have returned
an
object that may be cast to the appropriate BioJava object and then
handed
on to other objects that understand these (e.g. BioJava's SequencePanel)

If you would like to have a go with this, you will need to download and
install the AppLab client so you have the BSA client implementation (see
http://industry.ebi.ac.uk/applab/) and also the BioJava addon (see
http://industry.ebi.ac.uk/applab/home/dist/addons/).

You'll find installation instructions in the appropriate INSTALL.* and
README.* files.

In principle, this bridge code should work with other implementations of
BSA and so (like NetGenics) we would be happy to discuss contributing it
to the BioJava repository. 


Yours,
Juha Muilu and Martin Senger
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 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
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