Invisible InChI's

Some InChI’s are short, such as that for methane: InChI=1/CH4/h1H4. Others are long (think crambin), and you don’t want to show them inline. Or you just want to show them anyway, but still want the chemistry to be understood. Here come the invisible InChI’s. 1 minute read

Pimp my JavaDoc

Jörg’s PhD book Data Mining und Graph Mining auf molekularen Graphen - Chemoinformatik und molekulare Kodierungen für ADME/Tox-QSAR-Analysen has a dump of the JavaDoc of the GroupContributionPredictor in JOELib (Figure 3.2, page 43). There are two nice things to the shown JavaDoc: 1. it has links to Wikipedia; 2. it has a Further Reading section. less than 1 minute read

Is that Jmol in that D-Wave demo?

Slashdot reported on D-Wave’s recent demo of their 16-qubit quantum computing system. Video’s of the demo can be watched on Google Video. The second video demonstrates the use of the machine in similarity searching: less than 1 minute read

Writing up my PhD introduction chapter...

The last twelve months or so, I have been doing two jobs (excluding hobbies of mine, such as Chemical blogspace): my postdoc in the group of Christoph Steinbeck on computer aided structure elucidation, and finishing my PhD. The topic of my PhD is about the interplay between chemoinformatics and chemometrics: the first being strong in dealing with molecular structures, the latter strong in data analysis and mining, originally on experimental data. Really, I focused on a few existing problems, such as how to represent and analyze large libraries of crystal structures, the use of NMR spectra in QSAR studies, and two more practical problems regarding reproducibility of scientific results, which includes communication of data, and transferability of algorithms. Actually, I also studied fragment mining in QSAR for a set of transfactants, but that has not lead to firm results yet. less than 1 minute read

CDK Workshop - Days #3 and #4

Days #3 and #4 of the CDK Workshop have been quite busy indeed, and I have not been able to summarize them so far. After a rather interesting day #2, the third day was the last one with scheduled presentations. Kai Hartmann showed how he used the CDK in his systems biology research, and contributed the code he wrote to predict Gibbs energies based on fragment contributions. Miguel Rojas showed his MS prediction work, which is based on the CDK too. 1 minute read

RSC: the first publisher to go semantic!

Just announced: the RSC goes semantic ! Colin Batchelor was here at the CUBIC last autumn, where we discussed issues involved, mostly relating to experimental section of organic chemistry syntheses, and NMR and MS spectra in particular, so I knew that this was coming our way. The announcement writes: 1 minute read

CDK Workshop - Day #2

Because of other obligations, I was unable to attend the first day of the CDK Workshop, though Christoph had set up Skype so that at least I could hear the talks from Prof. Berthold (Konstanz, Germany) about KNIME and Prof. Zielesny about CDK-Taverna. 2 minute read