Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Virginia Tech's System X supercomputer provides super tool for simulation of cell division

31.01.2007
Virginia Tech researchers in computer science and biology have used the university's supercomputer, System X, to create models and algorithms that make it possible to simulate the cell cycle -- the processes leading to cell division. They have demonstrated that the new mathematical models and numerical algorithms provide powerful tools for studying the complex processes going on inside living cells.

Biologist John Tyson, who studies the cell cycle, is a leader in applying mathematical models in molecular cell biology. However, comparing the results of a mathematical model to experimental data is difficult because mathematical results are quantitative (numbers) while much experimental data is qualitative (trends). The mathematical biologist must figure out how to set the numerical values of the ‘parameters’ in the model equations in order to create an accurate representation of what is going on inside the cell. A simple example is the conversion between Fahrenheit and Celsius temperatures, said mathematician Layne Watson. "You could use several pairs of Fahrenheit and Celsius readings for the same temperature, and try to deduce the formula for converting between the temperature scales."

Previously, Tyson worked with simpler models whose parameters could be determined by trial and error, a process modelers call "parameter twiddling." But he and his coworker, Kathy Chen, wanted to characterize all the protein interactions regulating the cell cycle of budding yeast (the yeast cells familiar to bakers and brewers, and a favorite organism of molecular biologists, as well). "Such fundamental research on the cell cycle of budding yeast provides a basis for understanding the reproduction of human cells and is relevant to the causes and treatment of cancer, to tissue regeneration, and to the control of many pathogens," Tyson said.

For the budding yeast cell cycle, the experimental data consists of observed traits of 130 mutant yeast strains constructed by disabling and/or over-expressing the genes that encode the proteins of the regulatory network. The model has 143 parameters that need to be estimated from the data. "That is a big problem," said Watson. "You can't do that by hand. You can't even do it on a laptop. It takes a supercomputer."

In fact, it required more than 20,000 CPU hours on System X, a 2200 processor parallel computer, using two new algorithms, DIRECT (DIviding RECTangles) and MADS (Mesh Adaptive Direct Search), to estimate the 143 parameters.

"With a tool like this scientists can spend more time working on the model and less time twiddling parameters," said Tyson.

The research is due to appear in 2007 in the Journal of Global Optimization, in the article "Deterministic Parallel Global Parameter Estimation for a Model of the Budding Yeast Cell Cycle," by Thomas D. Panning, Layne T. Watson, Nicholas A. Allen, Katherine C. Chen, Clifford A. Shaffer, and John J. Tyson.

Panning, who is from Tulsa, Okla., received his master of science in computer science in May 2006 and is currently working as a programmer in Germantown, Md. Watson, of Blacksburg, is professor of computer science in the College of Engineering and professor of mathematics in the College of Science. Allen, who is from Columbia, Md., received his Ph.D. in computer science in November 2005 and is now with Microsoft. Chen, of Blacksburg, is a research scientist biological sciences in the College of Science. Shaffer, of Newport, is associate professor of computer science. Tyson, of Blacksburg, is a University Distinguished Professor of biological sciences.

The Virginia Tech computer science team created massively parallel versions of a deterministic global search algorithm, DIRECT, and a deterministic local search algorithm, MADS, to do the twiddling, and then combined the results. "A deterministic global search algorithm systematically explores the parameter space, finding good values," Watson said. "Then the local search algorithm improves the values from the starting points found by the global algorithm."

The parallel computer programs can now be used by others for similar problems. "The parameters found for the budding yeast cell cycle model are good until the next scientist invalidates them with new experimental data. That could be years from now or next week. That's the way science works," says Watson.

Susan Trulove | EurekAlert!
Further information:
http://www.vt.edu

Further reports about: Supercomputer Watson algorithm cell cycle computer science mathematical

More articles from Life Sciences:

nachricht Topologische Quantenchemie
21.07.2017 | Max-Planck-Institut für Chemische Physik fester Stoffe

nachricht Topological Quantum Chemistry
21.07.2017 | Max-Planck-Institut für Chemische Physik fester Stoffe

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Manipulating Electron Spins Without Loss of Information

Physicists have developed a new technique that uses electrical voltages to control the electron spin on a chip. The newly-developed method provides protection from spin decay, meaning that the contained information can be maintained and transmitted over comparatively large distances, as has been demonstrated by a team from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute. The results have been published in Physical Review X.

For several years, researchers have been trying to use the spin of an electron to store and transmit information. The spin of each electron is always coupled...

Im Focus: The proton precisely weighted

What is the mass of a proton? Scientists from Germany and Japan successfully did an important step towards the most exact knowledge of this fundamental constant. By means of precision measurements on a single proton, they could improve the precision by a factor of three and also correct the existing value.

To determine the mass of a single proton still more accurate – a group of physicists led by Klaus Blaum and Sven Sturm of the Max Planck Institute for Nuclear...

Im Focus: On the way to a biological alternative

A bacterial enzyme enables reactions that open up alternatives to key industrial chemical processes

The research team of Prof. Dr. Oliver Einsle at the University of Freiburg's Institute of Biochemistry has long been exploring the functioning of nitrogenase....

Im Focus: The 1 trillion tonne iceberg

Larsen C Ice Shelf rift finally breaks through

A one trillion tonne iceberg - one of the biggest ever recorded -- has calved away from the Larsen C Ice Shelf in Antarctica, after a rift in the ice,...

Im Focus: Laser-cooled ions contribute to better understanding of friction

Physics supports biology: Researchers from PTB have developed a model system to investigate friction phenomena with atomic precision

Friction: what you want from car brakes, otherwise rather a nuisance. In any case, it is useful to know as precisely as possible how friction phenomena arise –...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Closing the Sustainability Circle: Protection of Food with Biobased Materials

21.07.2017 | Event News

»We are bringing Additive Manufacturing to SMEs«

19.07.2017 | Event News

The technology with a feel for feelings

12.07.2017 | Event News

 
Latest News

NASA looks to solar eclipse to help understand Earth's energy system

21.07.2017 | Earth Sciences

Stanford researchers develop a new type of soft, growing robot

21.07.2017 | Power and Electrical Engineering

Vortex photons from electrons in circular motion

21.07.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>