Science Scope

First software simulation of an entire organism created

Posting in Cancer

Scientists have created the first software simulation of an organism, spelling a future of computerized laboratories and computer-aided biological design.

Experiments can take a long time, and that is part of the reason why we haven't yet found a cure for diseases like cancer or Alzheimer's.

But a new breakthrough may someday help speed up that quest.

Scientists at Stanford University and the J. Craig Venter Institute (named for the genome pioneer) have created the first software simulation of an entire single-celled bacterium. This achievement foretells a future in which computerized laboratories could run many thousands of experiments faster than is possible now.

The simulation was presented in the journal Cell.

How it works

The researchers created a model of Mycoplasma genitalium, which lives in the human respiratory and genital tracts. With 525 genes, it has the smallest genome of any independent organism. (Compare that to the 4,228 genes in E. coli.)

Using 1,900 experimental observations of the cell from 900 studies, they created the software model, which requires 128 computers to run. The model shows the complete life span of the cell and demonstrates how the 28 types of molecules within it -- DNA, RNA, proteins and more -- interact.

Models simulating individual cellular functions such as metabolism and protein synthesis already exist. This simulation stitches together a series of modules that mimic various cell functions to create the software organism. The leader of the new research, Dr. Markus W. Covert, an assistant professor of bioengineering at Stanford, told The New York Times.:

“The major modeling insight we had a few years ago was to break up the functionality of the cell into subgroups, which we could model individually, each with its own mathematics, and then to integrate these submodels together into a whole. It turned out to be a very exciting idea.”

What this breakthrough means for the future

The work of Dr. Covert and his team represents a milestone in the field of computational biology, which is known for achievements such as the creation of a synthetic life form, which was a bacterial genome created by a team led by Venter.

As James M. Anderson of the National Institutes of Health told Stanford News Service, "Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and, ultimately, to inform new approaches for the diagnosis and treatment of disease."

Right now, a lot of research consists of pinpointing a specific gene in an experiment to see what happens. But with cellular software simulation, researchers can see how multiple genes react in the experiment.

Additionally, this breakthrough could open a door to computer-aided design (CAD) in biology. So far, CAD has revolutionized fields such as aeronautics and civil engineering by slashing the amount of time spent on trial and error in design.

Computational models like the one made of M. genitalium could help guide experiments in biology and in the creation of new microorganisms. For instance, they could help design bacteria or yeast created specifically to mass-produce pharmaceuticals.

But we're not quite there yet: Dr. Covert told The Times, “Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data."

Related on SmartPlanet:

via: Stanford News Service, The New York Times

photo: Illustration by Erik Jacobsen/Covert Lab

Share this

Laura Shin

Features Editor

Laura Shin has been published in The New York Times, The Wall Street Journal and The Los Angeles Times, and is currently a contributor at Forbes. Previously, she worked at Newsweek, the New York Times, Wall Street Journal and LearnVest. She holds degrees from Stanford University and Columbia University's Graduate School of Journalism. Follow her on Twitter. Disclosure