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 Molecular Force Sensors
20.09.2017 | Max-Planck-Institut für Biochemie

nachricht Foster tadpoles trigger parental instinct in poison frogs
20.09.2017 | Veterinärmedizinische Universität Wien

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!

When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.

Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...

Im Focus: Fast, convenient & standardized: New lab innovation for automated tissue engineering & drug

MBM ScienceBridge GmbH successfully negotiated a license agreement between University Medical Center Göttingen (UMG) and the biotech company Tissue Systems Holding GmbH about commercial use of a multi-well tissue plate for automated and reliable tissue engineering & drug testing.

MBM ScienceBridge GmbH successfully negotiated a license agreement between University Medical Center Göttingen (UMG) and the biotech company Tissue Systems...

Im Focus: Silencing bacteria

HZI researchers pave the way for new agents that render hospital pathogens mute

Pathogenic bacteria are becoming resistant to common antibiotics to an ever increasing degree. One of the most difficult germs is Pseudomonas aeruginosa, a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Molecular Force Sensors

20.09.2017 | Life Sciences

Producing electricity during flight

20.09.2017 | Power and Electrical Engineering

Tiny lasers from a gallery of whispers

20.09.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>