I know I am lagging behind things... been busy and did not have time to reply to everyone yet. Some TOREPLY's go back more then a month. Sorry about that!

Some of the things on my TODO list (in random order): Bioclipse2 bug fixes, CDK patch reviewing (e.g.
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Last of my writing on the CDK Workshop. It was great fun meeting all the CDK developers and users, and thanx to everyone for all that they contributed, in particular during the unconference part! Yesterday, I had a travel day, and slept 12 hours in one go last nite. This leaves me with a long list of follow emails, CDK patches and many other things to catch up with. But it was more than worth it.

I wrote about my course material, and now complement that with the (three) slides:

CDK Workshop 2009 Slides Publish at Scribd or explore others: Research cdkws2009 cdk

The second CDK Workshop day started off with application presentations, which are well covered by Chris' blog posts:John van Drie’s talk on CDK in Virtual Drug Discovery,Asad Rahman on Small molecules and reaction mechanism - Rewiring the enzyme space, andOliver Karch about Molwind - Using CDK to Visualize Molecule Spaces in a Geospatial Context. You can also find coverage on Twitter by Jim and Nico.

The afternoon we had a more development oriented unconference.
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Coverage on Planet CDK, Twitter #cdkws2009, Friend Feed's CDK room, and on this Wiki page. Chris blogged too.

CDK Workshop 2009 Intro Course Material Publish at Scribd or explore others: Research chemistry cheminform
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The identity of domoic acid has been under discussion (see here, here and here).
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I just released CDK 1.2.1 (aka The CDK Workshop 2009 Release), which is now available for download from SourceForge. The source can be found in our Git repository. The changes since 1.2.0 are mostly bug fixing, new unit tests, and minor clean up here and there: Fixed bug 2714283, which properly throws an exception when rings are not closed properly. If a ring is not closed with the appropriate ring number, InvalidSmilesException is thrown.

In preparation of the CDK workshop next week, here is a small Bioclipse2 script to calculate the XLogP value for a given SMILES, using the a CDK-based XMPP service:

Earlier in this series:Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in JmolBioclipse2 Scripting #2: searching PubChem

Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML.

The latter is particularly interesting, as I do not know how to work that out...
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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