chem-bla-ics: July 2007

Further Bioclipse QSAR functionality development

I had some time to work some more on the QSAR functionality in Bioclipse. There is still much to do, but it is getting there. The calculation of a QSAR descriptor data matrix

This screenshot shows that multi-resource selection is now working, and that the calculation is now a Job.

Jul

OSRA: GPL-ed molecule drawing to SMILES convertor

Igor wrote a message to the CCL mailing list about OSRA:We would like to announce a new addition to the set of chemoinformatics tools available from the Computer-Aided Drug Design Group at the NCI-Frederick. OSRA is a utility designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES.

Jul

Screencasts for life science informatics

Deepak blogged about screencasting for bio topics, concentrated at bioscreencast.com of which he is co-owner. I guess it is like a YouTube for bioinformatics thingies. Jean-Claude picked this up very quickly (seen on Cb? At least I did.), and already uploaded a screencast, demoing JSpecView written by Robert. I wonder if he will upload the screencasts he made for Bioclipse too? (hint, hint ...

Jul

The CDK data model #1

The Chemistry Development Kit has a rich set of data classes, each of which is defined by an interface. While the classes for atoms, bonds and a connectivity table are fairly straightforward, but beyond that it is sometimes not entirely clear. I will now discuss all interfaces in a series of blog items. I'll start with the IChemFile. Christoph, please correct me if I move to far away from our Notre Dame board sketch.

IChemFile

The IChemFile is the class to hold a chemical document, e.g.

Jul

The Open Science Notebook 10 years ago

So, with all these people blogging about the Open Science Notebook (yes, each word is one distinct blog) it is worth looking back in time. To make clear what I put under the OSN: a notebook in which experimental details and outcome are written down.

Jul

CDK Literature #2

Second in a series of articles summarizing articles that cite one of the main CDK articles for CDK News. The first CDK Literature was already half a year ago, so it was about time.

Bioclipse

Nothing much I have to say about that. Just browse my blog and you'll see that it heavily uses CDK, JChemPaint and Jmol. See also the Bioclipse blog.

Jul

Inter- and Extrapolation: the NMR shift prediction debate

Chemical blogspace has seen a lengthy discussion on the quality of a few NMR shift prediction programs, and Ryan wanted to make a final statement.

Jul

That big pile of paper...

Everyone of use knows that big pile of paper on your desk that contains the things we want to read, scan or just browse. I even have an electronic equivalent. Another pile contains leaflets and glossy folders from conferences, like the ACS meeting in Chicago. OK, going to get rid of those last ones, and will shortly put the links here.

The first leaflet is from Chemistry Central, one of the open access publishers.

Jul

Standing on the shoulders of ... the Blue Obelisk

The Seven stones wondered what to do with a petaflop in science, in response to Declan's The petaflop challenge in Nature. Declan discusses in this commentary the increase in computing power and the necessity of parallel programming to make use of it. Now, I do have some ideas (e.g. enumerating metabolomic space, mining the RDF graph of our collective biological and chemical knowledge base for the one hundred most supported contradictions), but that is not what I want to talk about.

Jul

Atom typing in the CDK

Atom typing is one of principal activities in chemoinformatics. Atom types provide additional information that cannot be derived from the connection table that is being used, or may define what force fields terms should be used. This makes perception of atom types very important.

The CDK has a few places where atom types are perceived. The HydrogenAdder and ValencyChecker are two examples.