After a discussion on starting development releases for CDK on cdk-devel, the discussion continued on the state of the CDK atom typer . Dan and Rajarshi have done tests in the past against PubChem and its DTP/NCI subset. Rajarshi made his analysis part of CDK Nightly, and provides but a summary (which seems broken: zero fails) and a detailed list.

I reported earlier on how to compare unit test results between CDK trunk and a branch . Later, I noted that the diff typically overestimates the fail count, when unit tests had been moved to a different module. Therefore, a sort has to be added.

The MetWare components are slowly coming together. The RAW data upload facility prototype went into beta stage, while the SKOS has proven really useful for various things.

Today Ola, Jonathan and I have a mini-hack session on getting JChemPaint support ported from Bioclipse1 to Bioclipse2.

Via Carbon-Based Curiosities’s blogroll I found a number of new blogs (on top of the list I posted yesterday), and just added them to Chemical blogspace.

bbgm was rethinking software access.

Via Rich’ blog, I was informed about the work by goesLightly on CampDepict, a Ruby-based application which uses the CDK for SMILES parsing and 2D diagram generation. With cdk-20060714.jar it’s using pretty ancient code, and I have not seen a screenshot.

Some publishers hesitate a bit, but others go full speed ahead into the electronic publishing era.

Two companies recently showed two things:

While I do not agree in details on the statement made by Klaus, I agree with his intentions, and happy to propagate the mantra, like others did before me:

Today starts the MetWare developers meeting, hosted by Steffen Neumann, at the Leibniz-Institut für Pflanzenbiochemie. Steffen’s group and the Applied Bioinformatics group where I now work, are co-developing an opensource platform for metabolomics data management.