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.
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.
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
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.
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.
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.
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). The method is based on earlier
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.
An InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.
As of April 3, I will be working as postdoc in the group of Christoph Steinbeck at the Cologne University BioInformatics Center, or simply CUBIC, for a year. Though no exact plans have been decided upon, the work will include CDK, CML, ontologies, Bioclipse, semantic web technologies, Jmol, and other interesting things. Research areas will at least include QSAR, but I hope to touch bits of bioinformatics too.