Computer Simulation of Entire Organism Could Speed Disease Research

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Researchers at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism, a step toward speeding up research of treatments for various diseases, such as cancer or Alzheimer's disease, the New York Times reports.

On Friday, the simulation was published in the journal Cell.

Simulation Details

The simulation includes all of the genes and known gene functions of a single-cell bacterium that inhabits the genital and respiratory tracts.

It runs on a cluster of 128 computers and charts the interactions of 28 categories of molecules, such as:

  • DNA;
  • RNA;
  • Proteins; and
  • Small molecules known as metabolites, which are generated by cell processes.

The researchers used object-oriented programming, which has a similar design to modern software systems. The simulation involves a series of modules that mimic the functions of a cell, similar to how modules used by software designers pass data and instructions back and forth.

Researchers validated the accuracy of the simulation with data from more than 900 scientific papers.

Despite modeling the simplest biological system, researchers say the simulation is pushing the limits of their computers.

Markus Covert -- assistant professor of bioengineering at Stanford -- said, "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."

Implications

The software is expected to help researchers increase the pace at which they can conduct experiments by:

  • Speeding up the early stages of screening for new compounds; and
  • Helping create sufficiently accurate models that will help researchers develop a new understanding of basic cellular principles (Markoff, New York Times, 7/20).

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