The SWT JChemPaint (viewing) widget

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

less than 1 minute read

Graphical overview of my bookmarks

Deepak informed me about Wordle via a FriendFeed notice, which can make nice visualisations of tag clouds. Here’s the one for my del.icio.us account:

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Recovering full mass spectra from GC-MS data #2

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. At the same time, I notice that profiles are not as clean as before, but that’s where the peak fitting with (Modified) Gaussians come into play.

less than 1 minute read

Recovering full mass spectra from GC-MS data

One aspect not covered in detail by the ongoing discussion on unit testing quality control for scientific software, is detecting regressions. This is 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.

5 minute read

Good Scientists Pimp there Research (was: Damn, I'm boring...)

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.

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Finding differences between IChemObjects #2

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.

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Finding differences between IChemObjects

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!

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