1st complete computer model of an organism produced

In a breakthrough effort for computational biology, the world’s first complete computer model of an organism has been completed by Stanford researchers.

The team is led by Markus W.Covert, assistant professor of bioengineering and consists of

• Jonathan R. Karr
• Jayodita C. Sanghvi
• Derek N. Macklin
• Miriam V. Gutschow
• Jared M. Jacobs
• Benjamin Bolival Jr.
• Nacyra Assad-Garcia
• John I. Glass

Their paper titled A Whole-Cell Computational Model Predicts Phenotype from Genotype is published in Cell Journal

They 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 world’s smallest free-living bacterium.

Source : Cell Journal

Mycoplasma genitalium is a humble parasitic bacterium known mainly for showing up uninvited in human urogenital and respiratory tracts. But the pathogen also has the distinction of containing the smallest genome of any free-living organism – only 525 genes, as opposed to the 4,288 of E. coli, a more traditional laboratory bacterium.

Even at this small scale, the quantity of data that the Stanford researchers incorporated into the virtual cell’s code was enormous. The final model made use of more than 1,900 experimentally determined parameters.

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.

The purely computational cell opens up procedures that would be difficult to perform in an actual organism, as well as opportunities to reexamine experimental data. In the paper, the model is used to demonstrate a number of these approaches, including detailed investigations of DNA-binding protein dynamics and the identification of new gene functions. The program also allowed the researchers to address aspects of cell behavior that emerge from vast numbers of interacting factors.

Several findings can be made from virtual model. These remain hypotheses until they’re confirmed by real-world experiments, but they promise to accelerate the process of scientific inquiry.

Much of the model’s future promise lies in more applied fields.

1. 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.
2. Computational models like that of M. genitalium could bring rational design to biology – allowing not only for computer-guided experimental regimes, but also for the wholesale creation of new microorganisms.
3. Bio-CAD could also lead to enticing medical advances – especially in the field of personalized medicine. But these applications are a long way off, the researchers said.
4. “This is potentially the new Human Genome Project,” Karr said. “It’s going to take a really large community effort to get close to a human model.”

Reference : Stanford News, Cell Journal

Tags: Bio, CAD, cell, computer, engineering, informatics, model, simulation, software