Friday, November 03, 2006

Bioclipse Workshop: short but productive

The Bioclipse Workshop has ended and, for just three days, turned out quite productive. We have first bits of scripting support for JavaScript using Rhino. At this moment the scripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that. An example script:
// to have short identifiers
Array =;
String =;
msgBox =;
DbfetchServiceServiceLocator =;

// get data
service = new DbfetchServiceServiceLocator();
strarray = service.getUrnDbfetch().fetchData("refseq:NM_210721", "refseq", "raw");

// make readable
str = new String();
for (i = 0; i < Array.getLength(strarray); i++) {
if (i != 0)
str = str + ("\n");
str = str + strarray[i];

// show

It's just a short example that uses webservice technology in Bioclipse to fetch a sequence.

QSAR support

QSAR support is getting along too, with a new DescriptorProvider extension point in trunk/ and work is progressing on a wizard that allows selecting descriptors and a CDK backend. The output of the wizard is a matrix resource, for which we already have a rich editor. A JOELib plugin has been suggested, as it has a good deal of QSAR descriptors too; Jörg, interested in doing a tiny bit of Bioclipse hacking?

A full proceedings is available online.


  1. Egon,

    can you give me a concrete hands on and how-to do it?
    I have now two weeks holiday and I am not available online. Beside of that I am still busy like hell with my (still temporary) job.
    You know I would like to contribute as much as possible, but I have to share my resources. So, any help is highly appreciated.


  2. Jörg, please have a look at this class, which is, yet, a dummy implementation for the CDK:

    and this interface the underlies it:

    The rest is up to us.