The workshop itself was phantastic – we had 40 participants with well balanced contributions from industry and academia. The first half day was dedicated to tutorials on various aspects of CDK, basic installation, our CDK and Oracle-based chemical search engine, scripting of CDK from within Bioclipse and CDK-based workflows in KNIME. The second day brought talks about science and applications based on CDK by John van Drie, Asad Rahman und Oliver Karch.  I reported earlier on those talks.

This official part was followed by a developers workshop in the format of an unconference.  Participants suggested topics on the fly and then voted with their feet. The topics that then made it where:

• Clojure
• Mining ChEMBL with CDK pharmacophore stuff
• Threading group
• Top 10 improvements (CDK WS 2009 unconference)
• JChemPaint/Rendering

all of which reported their results on the CDK wiki.

Another important outcome was a movement to join forces in creating and maintaining joint CDK-based plugins for KNIME and Bioclipse. There is a lot of synergy to be harvested. Licensing problems will need to be overcome but that seems doable.

While this is something that we have explicitly not tried to prevent; still it is kind of appalling to see it happen. My personal expectation on having my/our code being used by others was always that they would offer additional services and still acknowledge the original authors.

The case that we are currently seeing includes renaming and the pretension that the prodcut has been created by them (citation: iBioTech from InfoCom laboratories). The question here is of course: Is this covered by the Bioclipse license or not.

I was surprised that my first two attempts to dig into the Bioclipse license led into nowhere. There was no such thing as a LICENSE file in the top level directory in bioclipse trunk. The next thing to do was to look at the code of net.bioclipse.BioclipsePlugin.java, which in my opinion should contain a header clearly stating the license for this code. Nothing there.

But of course, the Bioclipse website has a full coverage of the license issues with Bioclipse. I would clearly say that the redistribution of a number of parts of Bioclipse, including CDK, requires the distributor to make it clear to the customer where the source code is available, which then automatically implies giving proper credit.

My feeling is that this is a case to further investigate.