Ola has been doing a good job of integrating BioMoby support into Bioclipse. Earlier he completed a GUI for running BioMOBY services, and added more recently a JavaScript wrapper too, using the Rhino plugin developed by Johannes.

For example:

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);

Today, he explained how to create convenience JavaScript shortcuts, to reduce the typing.

Screenshots and status of the Bioclipse-BioMoby work is available from the wiki.

This post was originally posted as https://chem-bla-ics.blogspot.com/2007/11/glueing-biomoby-services-together-with.html.