Chemoinformatics p0wned by cheminformatics...

Noel had a 40 people vote over chemoinformatics versus cheminformatics. What do you think?

less than 1 minute read

SVN commit hooks down for CDK and Bioclipse

SourceForge has been playing with system upgrades again, and in an attempt to debug the failing CIA commits on IRC, I reinstalled the hooks for CDK and Bioclipse, so that now all hooks seem to fail, including the email hook… Apparently, it is a known bug, e.g. see this bug report. I assume SF will fix this soon.

less than 1 minute read

Moving to Sweden: Improving CDK support in Bioclipse

This autumn I will end my current post-doc position at Plant Research International in the Applied Bioinformatics group and at Biometris (both part of Wageningen University) funded by the Netherlands Metabolomics Center (lot’s of vacancies), where I had a good time, and collaborated in several projects within the NMC with much pleasure.

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The CDK Community: Developers, Members, and Users

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).

2 minute read

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