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Archive for September, 2008

Nightly Build Site for CDK 1.2.x

Since we’re coming up to a 1.2 release (see Egons post) I’ve put up a nightly build site for the 1.2.x branch here so that we can track improvemens in the JUnit tests and various other code and documentation quality issues.

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I just updated the CDK Nightly build script so that it summarizes the state of unit test coverage. Currently, trunk has a total of 3215 methods (in 378 classes) that are missing unit tests. See the JUnit test summary for a module-wise summary.

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I’m in academia and I do cheminformatics. Recent collaborations, papers and funding issues in this field have made me think about the future of this research in this setting. This, and a thread discussing David Leahy’s talk on InkSpot Science at the Soton Open Science Workshop got me started on this post.

There are currently a number of groups and collaborations that are attempting to perform drug discovery without the large centralized infrastructure that is characteristic of this process. Examples of this include Jean Claude Bradley who runs the UsefulChem project and the Synaptic Leap as well as various academic labs. Also see Kozikowski et al

Cheminformatics plays a key role in drug discovery efforts at various stages. For example, identifying or prioritizing compounds from virtual libraries, predicting ADME profiles and side effects (e.g., hERG activation) and so on. I should stress that such computational methods don’t replace bench work – but they can certainly enhance it. More generally, we’re now faced with a deluge of data – and human eyeballs are not going to be able to handle this. And this is exactly the place that cheminformatics does it’s stuff.

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