Not long after I posted my view on things, John posted his reply on the ChemSpider/OpenData discussion. His comment was merely to illustrate an internal advice to some organization, which got accidentally leaked. Anyway, a must read, with two good links to further reading on open data licensing.

Neil wondered “what a Nature Chemistry paper should look like”, and asked the following questions. Below are my answers.

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.

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: