I arrived in Chicago yesterday afternoon. Much warmed than the cold Chicago the ACS promised me, so my winter coat was really not necessary. Is this global warming? Or was the ACS simply wrong? Anyway, very foggy indeed, just like the Chemistry World blog wrote: There were several other Dutch chemists on the plane, among which a few formed postdocs from Nijmegen, who I knew from the time I was still a M.Sc. student in organic chemistry.
I had some fun today with making prints of reservations etcetera for my trip to the ACS conference in Chicago. Went over to the website to make a print of the location of the hotel I am in. (Intercontinental Chicago: in case you want to leave me a message to meet up over breakfast or so.) Anyway, so at the ACS website I found a notice that the ACS Housing people closed down and that I should contact the hotel directly. Fine, no problem.
Chemists are picking up Yahoo Pipes, or, as Noel calls them, Pipeline Pilot for RSS feeds. I tend to agree, as the source of the workflows are closed, that is, at least require registering to the Yahoo webpage. Several chemical applications have been developed since. One was developed by Kermit who wrote an aggregator for mass spectrometry journal articles. And Mitch has set up a similar feature for ACS journals.
QDIS blogged about Bristol-Myers and AstraZeneca teaming up for a new drug called dapagliflozin. Now, dapagliflozin is, this week, the most used search keyword in Google, leading to Chemical blogspace. I wondered what the chemical structure of this compound is. The AstraZeneca and Bristol-Myers Squibb websites don’t say.
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. This has the downside that it has no explicit semantic meaning.
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.