Scripting BioMoby in Bioclipse

I have been working hard on a BioMoby plugin to get BioMoby into Bioclipse. The ultimate goal is to mix and match between local functionality and remote services, and I have created some sample scripts to assist with this. It is not much for the moment but demonstrates how Bioclipse can take advantage of the many services in BioMoby, both in the GUI and in the scripting language (currently based on Rhino).

A sample script that retrieves a sequence from GenBank via a Moby service, and translates it into FASTA-format using the local library BioJava, is provided below.

console = Packages.net.bioclipse.util.BioclipseConsole;
moby = Packages.net.bioclipse.biomoby.ui.scripts.MobyServiceScripting;
biojava = Packages.net.bioclipse.biojava.scripts.BioJavaScripting;

prot=moby.downloadGenbank("NCBI_GI","111076");
seq=biojava.parseString(prot);
fasta=biojava.toFasta(seq);

console.writeToConsole(fasta);


The ouput of the script is:

Calling service...
Done.
Read: 1 sequences. Returning first.
>gi|111076|lcl|D31461.0|D31461 T-cell receptor delta chain BDN7, thymus - mouse
ATYFCALMERVSRRGAPDKLVFGQGTQVTVEP
Rhino script done.

More information and other sample scripts are available on the net.bioclipse.rhino (formerly bc_rhino) plugin page on the Bioclipse wiki.