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Wednesday, August 04, 2010

Using Bioclipse to upload data to an OpenTox server

As part of a continuing mashup of Bioclipse and OpenTox, I sat down with Nina in Oxford to implement uploading molecules from within Bioclipse with JavaScript to OpenTox servers. This opens the route to calculate QSAR descriptors using the OpenTox API.

As, a result, you can (with the code at my laptop) now do (see this BSL script at MyExperiment):

// requires an unspecified Bioclipse development version

ds = opentox.createDataset("http://apps.ideaconsult.net:8080/ambit2/");

opentox.addMolecule(ds, cdk.fromSMILES("CCCCC[N+](C)(C)C"))
opentox.addMolecule(ds, cdk.fromSMILES("ClC(I)Br"))

opentox.deletaDataset(ds);

Make sure to check out the other stuff I have been doing with respect to OpenTox.