Craig James wants to make SMILES an open standard, and this has been received with much enthusiasm. SMILES (Simplified molecular input line entry specification) is a de facto standard in chemoinformatics, but the specification is not overly clear, which Craig wants to address. The draft is CC-licensed and will be discussed on the new Blue Obelisk blueobelisk-smiles mailing list.

Pierre pointed me to Google’s view:timeline feature, which shows the search results on a time line, by recognizing phrases like “on 25 September 2000…”. This is its view on the Chemistry Development Kit:

A couple of people now confirmed the problem with the ACS journal RSS feeds. Being back behind my desktop machine, I can post the obligatory screenshot: The feed for Chemical Biology shows 79 feed items and the first one was a Environ. Sci. Technol. paper.

I was just about to install Subclipse (for the millionth time), and googled for the update site details: Does anyone know how you can get Google pick up or how it detects the Download/UpdateSite/etc pages, shown as direct links below the primary hit? Are HTML <link> elements used for that? Or does it use certain meta data, microformats, …?

The second Programmeerzomer and the second summer of code for me, will end tomorrow with a presentation of Niels on his new JChemPaint code. The summer is over before you know it. One of the goals was making the JChemPaint editor Swing independent and more easy to integrate with SWT widgets. So, I hacked up the last bits of Bioclipse code.

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.