The second part of the morning session featured a presentation by Sirisha Gollapudi which spoke about mining biological graphs, such as protein-protein interaction networks and metabolic pathways. Patterns detection for nodes with only one edge, and cycles etc, using Taverna.

I arrived at the EBI last night for the Taverna workshop, during which the design of Taverna2 is presented and workflow examples are discussed. Several ‘colleagues’ from Wageningen and the SARA computing center in Amsterdam are present, along with many other interesting people. This afternoon is my presentation.

Peter is writing up a 1FTE grant proposal for someone to work on the question how automatic agents and, more interestingly, the blogosphere are changing, no improving, the dissemination of scientific literature. He wants our input.

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!