CDK-JChemPaint #2: rendering reactions

I posted earlier today a Groovy script to render molecules with CDK-JChemPaint 8. Now, the new JChemPaint rendering engine also contains the functionality to render reactions. So, I can also do:

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CDK-JChemPaint #1: rendering molecules

I reported earlier that the CDK-JChemPaint patch is now a clean add-on from the CDK releases. This means that you download cdk-1.3.4.jar and cdk-jchempaint-8.jar separately, put them in your class path, and get started with, for example, Groovy:

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New Blue Obelisk Exchange online at Shapado.com

StackOverflow has served as very well in the past couple of months with the Blue Obelisk Exchange. The BOx was taking advantage of a beta project of StackOverflow, and users of that program can switch to a payed plan after the beta phase was over. That moment is nearing, but the pricing model is just unrealistic for us. There were also some comments on the Blue Obelisk using proprietary software (see Stackoverflow not open source — not a problem?).

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OpenTox Virtual Seminar, Thursday April 1, 11.00 CEST

Today I gave a presentation of my research, the CDK, Bioclipse, and recent RDF work:

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Cleaner CDK Code #4: inheriting JavaDoc from super classes and interfaces

When you write a class implementing an interface or extending a super class, it is often the case that the API is identical. It would be nice to inherit the JavaDoc documentation, which is possible.

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ACS Boston: RDF Symposium update

The deadline for abstract submission for the ACS symposium on Semantic Chemistry with the Resource Description Framework has passed. Eleven independent abstracts made the deadline. Here’s what you can expect in Boston:

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CDK-Taverna paper published

It took a while, but the CDK-Taverna paper (doi:10.1186/1471-2105-11-159) which has been in preparation for a while in the CDK subversion repository, is now published. Christoph already wrote up a brief explanation in his blog:

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