An R-based genetic algorithm

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.

less than 1 minute read

Why ODOSOS is important

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. It was not until the alchemists started to properly write down procedures that it, as a science, took off. Now, with chemoinformatics in mind, we have the opportunity to write down our procedures in high detail.

1 minute read

Taverna Workshop, Day 1 Update

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. An example data she worked on is the Palsson human metabolism (doi:10.1073/pnas.0610772104); she mentioned that this metabolite data set contains cocaine :) Neil Chue Hong finished with an introduction on the OMII-UK which is co-host of this meeting.

1 minute read

Taverna Workshop, Hinxton, UK

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.

less than 1 minute read

How the blogosphere changes publishing

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. To make his work easy, I’ll tag this item pmrgrantproposal and would ask everyone to do the same (Peter unfortunately did not suggest a tag himself). Here are pointers to blog items I wrote, related to the four themes Peter identifies.

1 minute read

SMILES to become an Open Standard

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.

1 minute read

Google's view in history

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:

less than 1 minute read