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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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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.
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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.
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InChI's in LaTex and CDK News
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.
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The Cologne University BioInformatics Center (CUBIC)
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.
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How to make money from Open Source scientific software
Dan (the original Jmol author) has an interesting blog series: How to make money from Open Source scientific software I, II and III. Three more blog items are in the planning. The deal with how to make money from open source scientific software. He wants to be able to skeptically review the software in his field, hence open source. But open source software development, at least in chemistry, needs funding, because there are too few people working on such software on a voluntary basis.