They only simulated a small section for 5 milliseconds but that's quite lengthy when working at the nanoscale. The second article is a similar simulation on Blue Gene. A good sign of things to come. Sometimes I wonder whether we're simply waiting around for technology to reach a point where we can build the tools to conquer biology's complexity as most efforts to intervene simply lead right back to the seeming dead end of "basic research."
World's biggest heart model simulated at University of Montreal
January 17, 2008
Researchers from the Université de Montréal have used a supercomputer to conduct the largest-ever mathematical simulation of the electrical activity of a human heart – a 2 billion element model – to provide new insight into cardiac and other illnesses. Until recently, the world’s largest simulated hearts had a few million elements at most.
The UdeM simulation was up to 1,000 times more detailed than previous models and will enable new scientific discoveries that would never have been possible otherwise.
The computer on which the simulation was performed, a 768-processor SGI Altix 4700, is the largest shared-memory computing system in Canada. Operated by the Réseau québécois de calcul de haute performance (RQCHP), it is used by hundreds of Canadian researchers.
Mark Potse and Alain Vinet, of the UdeM’s Institute of Biomedical Engineering, routinely use 60 to 100 of these processors to run their simulations of the human heart. In late October, Potse and Vinet had the opportunity to use the entire SGI Altix system and its 1.2TB of shared memory to solve the largest, most detailed heart model ever.
Two weeks to simulate full heartbeat
The researchers simulated five milliseconds of activation in a tissue block that included some properties of a real heart, such as fibre running in different directions. The simulation solved a system of two billion equations a dozen times. The test took two hours. A full heartbeat, Potse says, would take two weeks to simulate and his team cannot claim use of the entire supercomputer for such lengths yet.
“The purpose of the test was to show that when the next generation supercomputers becomes available, researchers will be able to use it effectively,” said Vinet. “This type of model is increasingly difficult to solve when it is larger. It was far from evident that this test was going to work.”
With heart disease one of the leading causes of death in the Western world, discovering the electrical triggers of the various kinds of heart disease could lead to earlier diagnosis and new treatment breakthroughs. In order to understand what the mechanisms of the particular disease are, the heart must be modeled with enormous detail.
Once disease mechanisms are fully understood, scientists will be able to devise the best drug or the best cure — surgical or other remedies -- and doctors will be able to diagnose much more precisely. Without the use of computer models it can be hard to track the effects of a heart disease on the ECG.
About the Institute of Biomedical Engineering
The Institute of Biomedical Engineering offers a joint graduate program at the Université de Montréal’s Faculty of Medicine and its affiliated École Polytechnique. The Institute brings together interdisciplinary researchers from heath sciences to engineering to investigate a variety of biomedical issues. Website: www.igb.umontreal.ca.
About the Université de Montréal
Deeply rooted in Montreal and dedicated to its international mission, the Université de Montréal is one of the top universities in the French-speaking world. Founded in 1878, the Université de Montréal today has 13 faculties and together with its two affiliated schools, the HEC Montréal and École Polytechnique, constitutes the largest centre of higher education and research in Québec, the second largest in Canada, and one of the major centres in North America. It brings together 2,400 professors and researchers, accommodates more than 55,000 students, offers some 650 programs at all academic levels, and awards about 3,000 masters and doctorate diplomas each year. Web site: www.umontreal.ca.
SGI - Innovation for Results™ SGI (NASDAQ: SGIC) is a leader in high-performance computing. SGI delivers a complete range of high-performance server, visualization and storage solutions along with industry-leading professional services and support that enable its customers to overcome the challenges of complex data-intensive workflows and accelerate breakthrough discoveries, innovation and information transformation. SGI solutions help customers solve their computing challenges whether it's enhancing the quality of life through drug research, designing and manufacturing safer and more efficient cars and airplanes, studying global climate change, providing technologies for homeland security and defense, or helping enterprises manage large data. With offices worldwide, the company is headquartered in Sunnyvale, Calif. Web site: www.sgi.com.
University of Montreal
Large-scale simulations of cardiac electrical activity
Principal Investigator: Jeffrey Fox
Affiliation: Gene Network Sciences
Co-Investigators: Robert Miller, Gene Network Sciences, Gregery Buzzard, Gene Network Sciences, Fernando Siso-Nadal, Gene Network Sciences
Scientific Discipline: Life Sciences
INCITE allocation: 846,720 Processor Hours
Site: Argonne National Laboratory
Machine: IBM Blue Gene/P
Allocation: 846,720 processor hours
Links:
Content Source: INCITE Fact Sheet
Article Source: Technology News Daily
Slashdot Coverage: DOE Awards 265 Million Processor-Hours To Science Projects
Research Summary:
Catastrophic rhythm disturbances of the heart are a leading cause of death in the United States. Treatment and prevention of cardiac rhythm disorders remains difficult because the electrical signal that controls the heart 's rhythm is determined by complex, multi-scale biological processes. Recent advances in experimental technologies have allowed for more detailed characterizations of normal and abnormal cardiac electrical activity. This project will use INCITE resources for rapid testing of hypotheses for the initiation and maintenance of rhythm disorders. These large-scale computer simulations represent a promising tool to help identify the underlying electrical mechanisms for dangerous arrhythmias and to determine the effects of interventions, such as drugs, that may prevent or exacerbate these arrhythmias. The results of these simulations may help elucidate mechanisms of heart rhythm disorders that pose a significant health risk to the general public. An improved understanding of these disorders will help lead to safer and better treatments for patients.
