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Crop Biotech Update

First Complete Computer Model of an Organism Released by Stanford

August 3, 2012

Scientists from Stanford University's Department of Bioengineering have completed the world's first computer model of the bacterium Mycoplasma genitalium. The said organism is the world's smallest free living bacterium that usually inhabits the ciliated epithelial cells of the primate genital and respiratory tracts.

The research team, led by by Markus Covert, assistant professor of bioengineering, used data from more than 900 scientific papers to account for every molecular interaction that takes place in the life cycle of Mycoplasma genitalium.

The minimalism of the bacterium's genome has made it the focus of several recent bioengineering efforts. Nevertheless, even at this small scale, the quantity of data that the Stanford researchers incorporated into the virtual cell's code was still extensive. The final model made use of more than 1,900 experimentally determined parameters.

To integrate these disparate data points into a unified machine, the researchers modeled individual biological processes as 28 separate "modules," each governed by its own algorithm. These modules then communicated to each other after every time step, making for a unified whole that closely matched M. genitalium's real-world behavior.

View Stanford's news release at http://news.stanford.edu/pr/2012/pr-computer-model-organism-071812.html.