Nightly CDK builds now available

Rajarshi Guha has set a nightly build service for the Chemistry Development Kit (CDK). The output is pretty, but information rich: it includes results for the JUnit test, DocCheck, and PMD. The compiled jar and the corresponding JavaDoc can be downloaded, offering a cutting edge distribution for users.

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Protein support in Bioclipse using Jmol and the CDK

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:

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Download statistics for chemblaics components

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):

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Postgenomic.com maps upcoming conferences

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!

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The CDK data classes and change notifications

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.

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Getting Jmol's 'cartoon on' to work in Bioclipse

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 it with PDB properties for the atoms, strands and monomers.

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Mining the KEGG pathway database with self-organizing maps

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).

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