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 less than 1 minute read

OSRA: GPL-ed molecule drawing to SMILES convertor

Igor wrote a message to the CCL mailing list about OSRA: less than 1 minute read

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 … :) less than 1 minute read

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. 2 minute read

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. So, what did the OSN look like almost ten years ago? 1 minute read

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. 2 minute read

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. Down his blog item he had this quote from Jeff, discussing the use of the NMRShiftDB as external test set: 4 minute read