Jim reported about SPECTRa being in the news and ./ about Toward a 3D Search Engine. These two items have in coming that they deal with the article Ultrafast shape recognition for similarity search in molecular databases by Ballester and Richards (DOI:10.1098/rspa.2007.1823). The NewScientist wrote up their angle on it, with a quote from Henry Rzepa.
Nascent reported that Nature Network v2 has gone life. Never too anxious to try something new, I created an account and signed in. I even joined two groups: Bioinformatics and Semantic Web for the Life Sciences . But, when I tried to create a new group, the system fails. I promised me to send me email for confirmation. Tried it twice via my Sourceforge email account. No email.
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. Alt text for images One solution is to put the InChI as content of the @alt attribute of the HTML <img> element.
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. Now, the CDK already links to a bibliography for some time now.
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: Now, that screenshot does look like Jmol. The companies website does not give the answer, though Scott mentions C and Java front end software. So, let’s ask the source: Dear dr. Rose, is it Jmol what we see in that demo?
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.
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.
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: RSC Publishing, the publishing arm of the Royal Society of Chemistry, is pleased to announce a new initiative for its journals.
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. Today, Miguel Rojas and Stefan Kuhn discussed their research. Miguel showed the state of mass spectrum prediction using the CDK and the MEDEA plugin for Bioclipse.
The second day just started of the Open Source Meets Business, and now actually listening to the PHP talk, but here is a short update on day 1, which was the investment summit. It was not so crowded, but especially the talks from the venture capitalists were interesting. During lunch we actually talked to one in person, which was insightful. I will be putting up links to interesting sites mentioned during this conference on my delicious account.
Today at the OSMB we had again a good lunch again, and Rachel Sterne joined our table. She works at a New York based start up Ground Report, which is a news website where anyone, including bloggers, can post news stories. Not links to news stories, as on Slashdot, but actual news stories. Stories that can be committed are not restricted to any topic, or country, or whatever.
