Big leap in bio-engineering: scientists simulate an entire organism in software for the first time ever

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Scientists at Stanford University and the J. Craig Venter Institute — remember the Human Genome project — have simulated an entire organism in software for the first time ever.

Using a 128-node computing cluster, a team of scientists led by Stanford professor Markus Covert incorporated data from more than 900 scientific papers and 1,900 experiments to simulate every molecular interaction and the effects of all 525 genes of the smallest known free-living bacterium: the parasite Mycoplasma genitalium.

And, yes, that bacteria lives right where its name suggests.

Simulating a single cell division takes about 10 hours, according to Covert, and generates half a gigabyte of data. Not exactly big data, but then it is a very small organism. Adding more computing power should shorten the simulation time.

But the reason for building a bacterium in emulation?

“You don’t really understand how something works until you can reproduce it yourself,” says graduate student  and team member Jayodita Sanghvi.

Now that an entire organism has been simulated, researchers believe that Bio-CAD (computer-aided-design) will take a big leap forward. From understanding genes in isolation the scientists look forward to being able to study their interactions, which is an essential step to understanding key issues in health, disease, and growth.

As Max McClure wrote in a story published by Stanford’s news service:

CAD – computer-aided design – has revolutionized fields from aeronautics to civil engineering by drastically reducing the trial-and-error involved in design. But our incomplete understanding of even the simplest biological systems has meant that CAD hasn’t yet found a place in bioengineering.

The new simulation will help scientists understand biology better, and understand cells better, the researchers say. And it will help both speed up research and enable testing that just isn’t possible otherwise.

“If you use a model to guide your experiments, you’re going to discover things faster. We’ve shown that time and time again,” said team leader Covert.

But don’t get your hopes up too high for personalized medicine or helpful simulations of how medication will affect you before you actually have to take it. A fully simulated human being is still a long way off.

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