Jekyll2026-08-14T05:35:03+00:00https://chem-bla-ics.linkedchemistry.info/feed/by_tag/ambit.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenOxford, August 2010: eCheminfo Predictive ADME & Toxicology 2010 Workshop2010-03-22T00:00:00+00:002010-03-22T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2010/03/22/oxford-august-2010-echeminfo-predictiveThe first week of August I will attend the eCheminfo Predictive ADME & Toxicology Workshop (LinkedIn Event) for which I received a Bursary Award. It will be my first time in Oxford, and I am very much looking forward to it!

The meeting is also bound to be fun. I have not done much in the area of toxicology other than the more general QSAR/QSPR model building with chemometrics. But I have been recently taking to Nina and other of the OpenTox community, and started to play a bit with the data and computation API they are developing.

I started a Bioclipse plugin recently (see screenshot), and placed the source code in this bioclipse-opentox Git repository on Gitorious (my GitHub account is already over the formal limit). The functionality is still quite limited, and the manager currently only provides methods to download data sets (myexperiment:1192):

// query a service using the OpenTox API 1.1
// See: http://www.opentox.org/dev/apis/api-1.1

var service = "http://apps.ideaconsult.net:8180/ambit2/";

var datasets = opentox.listDataSets(service);
for (set=0; set<datasets.size(); set++) {
  var dataset = datasets.get(set);
  js.say("Downloading set: " + dataset);
  ui.open(
    opentox.downloadDataSetAsMDLSDfile(
       service, dataset, "/OpenTox/ambit" + dataset + ".sdf"
    )
  )
}

Behind this plugin is again the RDF plugin, as OpenTox uses RDF too, a few simple SPARQL queries was all that needed to be defined. And again, the Bioclipse pluigin code base is pretty small.

]]>Egon WillighagenQSAR plugin for Bioclipse getting in shape2007-06-27T00:00:00+00:002007-06-27T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2007/06/27/qsar-plugin-for-bioclipse-getting-inOver the last few weeks I continued the work on getting (descriptor-based) QSAR/QSPR implemented in Bioclipse. JOELib (GPL) and the CDK (LGPL) being two prominent opensource engines that can calculate molecular descriptors, and AMBIT a front-end.

To be able to do QSAR/QSPR model building from start to end in Bioclipse, I worked in April on an architecture for selecting descriptors . Being busy with so many things, it took me some time to get around to completing that, but here are the screenshots:

The funny characters and the whitespace is gone. Right now, it still only lists one provider, but I plan to add JOELib plugin soon. The list of actual descriptors is provided by the extension.

What Bioclipse then does, is have the extension calculate the descriptor values for the selected CDKResource in the BioNavigator using the selected descriptors. This will then create a new MatrixResource in the Bioclipse workspace (currently called qsarResult.jam), and which is opened in the Matrix editor:

There is still enough work left to do. For example, the columns are not yet labeled according to the descriptor name, and selecting more than one CDKResource in the navigator does not give a multirow matrix yet.

]]>Egon Willighagen