Two companies recently showed two things: open access and open data allow adding value adding value is easier by forking Rich’ MetaMolecular set up Chempedia which combines a substructure-searchable chemical Wikipedia. There is also a page to make links to new Wikipedia monographs.

The results for the Open Lab 2007 are out . I participated in this endeavor as judge, and read 75 of the 486 blog items, focusing on the sections chemistry, blogging, publishing, politics of science , and a number of blog items with few reviews when I passed them. I am happy to see that one of the chemistry submission I made myself made it into the anthology: the Depth-First item on SMILES and Aromaticity: Broken?

As promised , here is my list of submission for the Open Laboratory 2007: Open Data is critical for Reproducible Research If you ever made something fluoresce after you did a reaction with a transition metal… One For the Brave Fun with singlet oxygen SMILES and Aromaticity: Broken?

During my PhD I wrote a simple but effective genetic algorithm package for R. Because there was a bug recently found, and there is interest in extending the functionality, I have set up a SourceForge project called genalg. The package provides GA support for binary and real-value chromosomes (and integer chromosomes is something that will be added soon), and allows to use custom evaluation functions.

Pedro reminded me of the last call for Open Laboratory 2007, which prints the best blog items of 2007 in book form. The list of chemistry contributions is not so large yet, so go ahead and nominate some of cool chemical blog items of the last year. I will post my shortlist later this week.

That must be a record! Eric Jain wrote on public-semweb-lifesci:

I value ODOSOS very high: they are a key component of science, and scientific research, though not every scientist sees these importance yet. I strongly believe that scientific progress is held back because of scientific results not being open; it’s putting us back into the days of alchemy, where experiments were like black boxes and procedures kept secretly.

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.