An open source project is as good as its community. Jmol has a brilliant community, but CDK is not doing bad either, in general at least; some CDK projects could use some more user feedback, such as CDK-Taverna (site down at the time of writing, but see the blog).

There are actually quite a few things going on within the CDK Community. There are a few active or less active projects:CDK Library (The main and most well-known component))CDK-Taverna (just mentioned)CDK News (Not active enough, please contribute!)CDK Nightly (Rajarshi's nightly build and check service, for trunk/ and cdk1.0.x/)JChemPaint (For which a new version is being developed.) (Even withing the CDK Library, several threads are ongoing, but I will report on that at some later stage).

In addition to this Swing based screenshot of JChemPaint, here's a SWT widget in action (lower right corner):

Not quite as beautiful as the ChemWriter, but a start.
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Deepak informed me about Wordle via a FriendFeed notice, which can make nice visualisations of tag clouds.
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Steffen reminded me over email that the particular machine only has a 1 dalton accuracy, and that the 150ppm parameter setting is somewhat inappropriate. As seen yesterday, it works fine for larger peaks, but fails for low intensity peaks. So, I reran the centWave peak detection with 750, 1000 and 1250 ppm, and that indeed make XCMS recover many more metabolites, and, also important, with more extracted ion chromatograms per metabolite, yielding a more accurate mass spectrum.

One aspect not covered in detail by the ongoing discussion on unit testing quality control for scientific software, is detecting regressions. This the most important reason why unit testing is superior to random testing. Putting someone behind a keyboard to tests things is nice, but this process has to be repeated, as the testing has to be repeated over and over again. Just to make sure it works for whatever new input, for whatever refactoring, for whatever new cool feature.
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Define good. Let me say that up front. Good scientists, that is, if you say successful researchers are good scientists, secure good funding. Getting good funding requires doing the most relevant research (define relevant). Or, to put it bluntly, being a successful researcher requires to pimp your research. Doing boring research is nice for you, good for a Nobel prize if it turns out to have a cool spin off, but doesn't buy you research success.

CDK QSAR descriptors are not allowed to change the input [molecule|atom|bond], and I recently added a unit tests (rev 11138) for that to the abstract class AtomicDescriptorTest.

CDK trunk is getting into shape, thanx to the many people who contribute to this, and special thanx to Miguel for cleaning up his code related to charge, resonance, and ionization potential calculations!

At the moment, I am focusing at two issues:QSAR descriptors that change the input (causing other descriptors to randomly fail)Cloning of IChemObject (for which last week a rather serious bug was found) Until some days ago, the CDK had one main method to introspect IChemObjects: their toString()
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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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