Using the InChI and the new rdf.openmolecules.net website, it is now possible to tag molecules. And if you use Connotea for that, your tags will even show up on the rdf.openmolecules.net website. For example, at the time of writing, methane was tagged with alkanes and gas . The trick I use, is that the rdf.openmolecules.net gives every molecule a unique HTTP URL.
All start is difficult. The ACS must know that, but they still blame Google.
Amanda had a very nice post on Small molecules that modulate quorum sensing. It’s the perfect read for a Sunday morning, when you have a view looking down on Strasbourg from a hill in the Black Forrest. Biology fascinates me, particularly when small molecules are involved. And the molecular signaling used by these bacteria is just delightful. Make sure to read up on the small squids in 96-well plates too! (And we are worried about varkensflats!
Rich posted a nice quote the other day on the introduction of the forward pass in football some 100 years ago, and linked that to sciences. I commented with the remark that the outscoring is the problem: Just after that, I read this blog by Antony on survival-of-the-fittest chemical search engine. Even though the measurement of the score is easy, these statistics can easily be obfuscated.
The IUPAC/NIST team made a beta release of the next InChI software release: InChIKey A had heard about the InChIKey extension earlier, and it solves the issue some people have with the InChI: it is too long. Well, molecules can have many atoms indeed. It is important to realize the InChIKey is not a replacement: it simply is not unique. The collision probability is calculated to be rather small, though.
Peter has been doing an excellent job in advocating ODOSOS , and one of his posts even hit Slashdot. Meanwhile, blogspace has been flooded with dislike of the PRISM intiative (e.g. see also the other Peter’s blog ). The website is so sad, it is almost funny again; but on second thought, it is so sad, you wonder the world will end because of WOIII or because of a total halt of scientific progress.
Niels and I held a JChemPaint hack-a-thon today (the IRC log). We had a quite ambitious agenda: make the renderer modular make the controller modular make a controller interface with Swing + SWT implementations All this to make the JChemPaint editor module of the CDK more easily integrate with non-Swing widget environments.
If you, like me, already upgrade to Ubuntu Gutsy, and use nxclient for remote login (highly recommended, though proprietary code), you might run into the problem that the login no longer works, returning the message “Cannot find KDE environment.”. Ubuntu’s Lauchpad (generally an excellent service) was rather uncooperative and disregarded a bug report about the problem, I found the solution with grep -ri kde /usr/NX:
I just installed XCMS 1.9.2 on my Ubuntu system. XCMS is a GPL-ed R package for metabolomics data analysis.
Rich blogged about Firefly embedding MDL molfiles in PNG images , which I found really cool. Rich and Noel later showed how that metadata can be retrieved again , possibly with Python. But I did not like that Firefly could do this, and JChemPaint not. So, I started hacking. First I discovered I had to get rid of the use of JAI; then I had to adapt the JChemPaintPanel takeSnaphot() API to return a RendererImage;
Clustering and classification of crystal structures is hot. Parkin hit the front cover of CrystEngComm with a story on Comparing entire crystal structures: structural genetic fingerprinting (DOI:10.1039/b704177b). Now, the story itself, while rather interesting and well written, has three major flaws: