chem-bla-ics

Here are some quick download statistics for some of the chemblaics components. First Jmol. The new stable Jmol 10.2 was release just over a week ago, and this obviously boosted downloads, breaking the monthly download total of two earlier this year (source):

Statistics for the CDK include download numbers for the CDK library itself, but for JChemPaint, the CDK News, and several other packages too. Totals are at about 1/3rd of Jmol. Another new record, breaking an earlier record set in February 2003 (source):

Finally, I want to mention the overall download count for kfile_chemical was is much higher than I ever would have hoped for: 1125 in 7 months! Maybe I should ask to get this in the KDE extragear.

Update: fixed Jmol link.

I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC where I continued the work on proper protein support in Bioclipse using the CDK and Jmol:

The latter involves getting the CdkJmolAdapter, the interface between the CDK and Jmol, updated for changes since the Jmol as 3D viewer for CDK article in CDK News, the open access journal for CDK related projects.

Conference season is nearing. And just in time, Postgenomic.com added a conferences map showing locations of upcoming and recently finished conferences. Oh boy, do I want to set this up for chemoinformatics too!

Postgenomic.com makes use of the rel="conference" attribute for the <a> element. I'm not sure how they distinguish between upcoming and finished conferences (will need to check the source code).

The data classes of the Chemistry Development Kit are mutable, unlike those of Octet. This means that other classes may need to respond when the content updates. For example, a render class. CDK's ChemObject provides a notifyChanged() and addListener() methods for this. However, as was recently pointed out, while this is useful in editors, such as JChempaint, this is a performance killer in high-throughput sitations, such as descriptor calculation, or structure diagram generation runs.

Bioclipse 1.0 is to be released in May, and the cartoon on script command is still not working in the Jmol viewer. For those who do not know yet, Bioclipse is a cool Eclipse RCP based Java chemo- and bioinformatics workbench. To have a better idea what goes on inside Bioclipse, I wrote a new BioPolymer tree to show me the strands in the protein. After Ola wrote code to show properties for IChemObject's, I extended did with PDB properties for the atoms, strands and monomers.

The Self-organizing map (SOM) is a popular (again) and intuitive non-linear mapping method: it transforms a multidimensional space into two dimensions (normally: they are so easy to visualize). Latino and Aires-de-Sousa published a paper that uses this method to analyze the whole KEGG pathway database: Genome-Scale Classification of Metabolic Reactions: A Chemoinformatics Approach (DOI: anie.200503833).

While I was working on implementing proper author-given chain IDs in PDB structures for Jmol's mmCIF reader today, I thought it was interesting to mention the recent article Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors by Nabuurs (DOI: 10.1371/journal.pcbi.0020009, open access), working at the CMBI, two floors away from my former working location at the Radboud University Nijmegen.

Internet has the nice feature of bringing together people. This has helped many open source projects in the past. But it is also a convenient and cheap way to have conferences. Next month, the ChemConf 2006 conference will be held, and interested people only need to subscribe to a mailing list to participate.

The topic of this years ChemConf is Web-Based Applications for Chemical Education.