Open source Digital Bacteria

FiReaNGeL writes "Scientists have constructed a software capable of simulating organisms at the molecular, single-cell and population levels. The program, called AgentCell, will soon be available, open sourced under a BSD license. "With AgentCell we can simulate the behavior of entire populations of cells as they sense their environment, respond to stimuli and move in a three-dimensional world". The researchers have designed their digital bacterial system in modules, so that additional components may be added later - "The hope is that people will modify the code or add some new capabilities". AgentCell has possible applications in cancer research, drug development and combating bioterrorism. Lots of movies and pictures are available, along with a detailed press release describing the program."

Comments

Re:This is pointless

[macklin01]

There are many reasons. For one thing, not all physical quantities are easily and accurately measurable. But in a situation like this, you can measure whatever you simulated and gain new insights, right down to the molecular level. Chemical reaction rates in individual cells, intracellular pressures and mechanical stresses, the effects of different mutation rates, the distribution of nutrient concentrations both within the cells and between them, and so forth.

Then there's the issue of experimental control. Want to test the effect of a different mutation rate in gene X? No problem. Vary that effect in your model only and don't change anything else. There's some good science to be conducted once the numerical implementation and the biophysical models have been validated.

Then there's cost. You can run many simulations and obtain a vast amount of data in the same time and for much less cost than it would take to run a few physical experiments. So, run a few hundred computer sims to determine which physical experiments are worth conducting; now physical lab time is more focused and more efficient. -- Paul

Re:combating bioterrorism

[Daniel Dvorkin]

The thing is, anything that helps us fight infectious disease in general may also help with "combating bioterrorism." And a good simulation of the response of bacterial populations, which often show emergent behavior, respond to biochemical stimuli may very well be helpful in coming up with new methods of diagnosis and treatment. (For an understanding of why this is so, check out work on swarming behavior, and the research interests page of Leah Edelstein-Keshet, one of the leading researchers in the field.) I'm not any happier than you are about how the bioterrorism card is played in every grant application, but it really is one of many valid applications here.