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): less than 1 minute read

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! 1 minute read

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. 1 minute read

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. less than 1 minute read

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). less than 1 minute read

Uncertainty in NMR based 3D protein models

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. 1 minute read

Free online ChemConf 2006 conference

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. less than 1 minute read