Digital E.Coli

OK, judging by the number of people who've bookmarked the URL on del.icio.us I'm behind on picking up on this. My excuse is that systems biology - the modelling physical processes kind of systems biology, anyway - isn't really my thing.

One of the reasons for that is, well, I find it boring (I'm sure that lots of systems biologists find what I do boring, too, so hey). At least, I did find it boring: then I saw AgentCell, modestly subtitled "digital e. coli". Emonet et al. haven't created life in a virtual test tube quite yet but what they do have is a neato simulation of bacterial chemotaxis.

A quick aside for the bioinformaticians leaning compsci-wards (thanks to Wikipedia):

Chemotaxis is the phenomenon in which bodily cells, bacteria, and other single-celled or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food (for example, glucose) by swimming towards the highest concentration of food molecules, or to flee from poisons (for example, phenol).

The assays done in-silico on populations of these agents reproduce experimental data done on real life bacterium.

I think that what makes AgentCell more impressive than similar simulations to an outsider like myself is, sadly, the nice AVIs. That and the (relatively) easily understandable pathways involved. Let this be a lesson in presentation to all systems biologists.

AgentCell's source code was released yesterday, if you're interested in probing a little deeper. The relevant paper is in OUP Bioinformatics (subscription required), here.

Addendum: I've just read the press release from the University of Chicago. Let AgentCell also be a lesson in fantabulous hyperbole to all systems biologists:

The simulation, called AgentCell, has possible applications in cancer research, drug development and combating bioterrorism.

Combating bioterrorism?! Whatever you've got to do to get the funding, I guess....