Sunday, July 22, 2012

Computer grid simulates entire living organism

Simulation of life is something that sounds like science fiction or part of the popular film trilogy The Matrix. However, computers are getting increasingly powerful and have begun to find their way into the laboratories of biologists. Computers are able to calculate a lot more than us human beings, and are therefore often used to study protein or gene interactions. Because molecules inside a cell can come into contact with billions of other molecules, it is impossible for us to turn it into something that can be calculated beforehand, but computers can do some of the job for us. Now, scientists have proven capable of simulating an entire organism by simply using enough computing power.

M. genitalium
In order to make a model of an entire organism, the scientists took a bacterium that only possesses 525 genes, of which most functions are known to us. Other animals, such as human beings, have tens of thousands of genes, and are therefore impossible to model with the amount of computing power we currently have. The bacterium that was simulated by computers is called M. genitalium, and normally causes nasty diseases when infecting humans, despite being the smallest of all known bacterial species.

Special software and a grid of 128 computers made simulation of the bacteria and all its functions possible, according to the scientists. They showed that basic cellular processes required a lot of computing power and generated heaps of data. For example, division of a bacterium into two daughter cells cost 10 hours to calculate and generated 500MB of data. More complex biological processes are likely to require even more time and storage.

According to the scientists, they are the first ones to simulate an entire organism. They claim it will help us to study drug interactions: researchers merely have to feed drug data to the computer, after which its effects on the organism will be calculated. It will speed up drug development, but will also help us study biological processes in more detail. It remains to be seen when more complex organisms will be modelled. As said, M. genitalium is very simple with just 525 genes; other bacteria such as E. coli have well over three thousand genes. Simulating a human cell will be even more difficult to achieve.

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