chem-bla-ics

Earlier I reported about postgenomic.com, and needed some diversion from my manuscript work (could no longer think straight about the article I'm working on). So time for some reading up on new technologies. Timing was perfect, because the source code of postgenomic.com got just uploaded to SourceForge SVN.

Though the author marks it as not-well-documented and alpha, I was quite happy to see a clear modularisation, and good enough docs to get me started with InChI support: if it can do mining for papers on DOIs, then it can do mining for InChI's too. Here's the result:

It does not show which blog items cite this compound, not does it extract some molecular info from PubChem, but I'm happy with the result of four hours of hacking.

Earlier I already reported that student text books were picking up Jmol as 3D viewer. Now, Nature Structural & Molecular Biology reports (DOI: 10.1038/nsmb0206-93) that they picked it up too, using FirstGlance in Jmol (thanx Peter, for reporting this on the Blue Obelisk mailing list!). And, thanx Eric, for acknowledging the hard work of the Jmol developers.

For the past few weeks I have been working on a review article, which will contain a section with new QSAR/QSPR descriptors published in the period 2000-now.

OpenSource, OpenData and OpenStandards are not as strong in chemoinformatics as they are in bioinformatcs, where it is common knowledge that sharing is a good. Today, the JCIM published on the web an article about the Blue Obelisk movement, which promotes these three idealogies.

Several open source projects participate, amongst which the CDK, Jmol, JOELib, OpenBabel, Chemical Markup Language, Bioclipse and Kalzium.

You might have read earlier posts in this blog on CMLRSS, and received a question today on how to integrate CMLRSS with blogs on blogspot.com. Now, current CMLRSS feeds are normally generated with customized scripts, often directly from a database.

So, here's my attempt to include CML in a blogspot.com blog.

Gemma Holiday's article on CMLReact was published in the january issue of the JCIM (DOI 10.1021/ci0502698), which seems to be marked as sample issue right now. She used CMLReact as data format for MACiE (see DOI 10.1093/bioinformatics/bti693), a database of 100 enzyme reactions, with fully annotated reaction mechanisms, making this an remarkable and insightfull database.

Roland Krause discussed today in his blog Notes from the Biomass an interesting website: postgenomic.com. This website, still marked BETA, mines blogs in the field of genomics and extract noteworthy statistics from it: which articles are cited in those blogs.

For example, the most discussed article is Kai Wang's Gene-function wiki would let biologists pool worldwide resources in Nature. Additionally, postgenomic.com links to the DOI, PubMed and shows which blogs discuss the article.

Wow.

I was very pleased to read today that Kalzium, one of the projects that participate in the Blue Obelisk, got awarded! Cheers, Carsten!

Technorati tags: KDE Kalzium Blue Obelisk chemistry

If you have read my previous post and visited that other blog, you might have noted the Technorati keywords. Or tags, really, as explained in this rel="tag" microformat. Adding them to blog items, will enable indexing by Technorati, one of the bigger blog search engines. So, from now on, you'll see these tags in my items too, hoping they don't get annoying. No idea, btw, how blog planets respond to them...

I never got around to mentioning this blog, but YAKAFOKON is a nice blog about, as the titel already says, bioinformatics, the semantic web and social networks. Nice to read, and interesting comments on the function and features of the internet and how they relate to bioinformatics, and science in general.