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Scientists at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism, a humble single-cell bacterium that lives in the human genital and respiratory tracts.
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the work was a giant step toward developing computerized laboratories that could carry out many thousands of experiments much faster than is possible now, helping scientists penetrate the mysteries of diseases like cancer and Alzheimer’s.
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This kind of modeling is already in use to study individual cellular processes like metabolism. But Dr. Covert said: “Where I think our work is different is that we explicitly include all of the genes and every known gene function. There’s no one else out there who has been able to include more than a handful of functions or more than, say, one-third of the genes.”
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The simulation, which runs on a cluster of 128 computers, models the complete life span of the cell at the molecular level, charting the interactions of 28 categories of molecules — including DNA, RNA, proteins and small molecules known as metabolites, which are generated by cell processes.
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They called the simulation an important advance in the new field of computational biology, which has recently yielded such achievements as the creation of a synthetic life form — an entire bacterial genome created by a team led by the genome pioneer J. Craig Venter. The scientists used it to take over an existing cell.
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A decade ago, scientists developed simulations of metabolism that are now being used to study a wide array of cells, including bacteria, yeast and photosynthetic organisms. Other models exist for processes like protein synthesis.
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“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,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that.”
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scientists chose an approach called object-oriented programming, which parallels the design of modern software systems. Software designers organize their programs in modules, which communicate with one another by passing data and instructions back and forth.
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“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,”