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Monday, November 05, 2007

Glueing BioMoby services together with JavaScript in Bioclipse

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 shortcut, to reduce the typing.

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