HPCwire: Researchers Improve Modeling of Cardiac Arrhythmia

Since 1986 - Covering the Fastest Computers in the World and the People Who Run Them

HPCwire >> Off the Wire

November 09, 2009

Researchers Improve Modeling of Cardiac Arrhythmia

Nov. 9 -- The Edinburgh Parallel Computing Centre (EPCC) at the University of Edinburgh, in collaboration with Dr Gernot Plank of the Oxford e-Research Centre (OeRC), has been awarded funding to optimise heart-modelling software. If successful, this work will enable much greater integration of computer simulation with the operating theatre and could, ultimately, lead to personalised medicine.

Medical science is increasingly turning to computational models to study the possible effects of drugs and surgical interventions, before moving on to patient trials. One active area of research is in heart modelling. The structure of a patient's heart can be obtained through MRI scans, this data is then placed on a computer and used to construct a model heart. Researchers can study the electrical activity in this model heart, which controls heart beats. Problems such as arrhythmia can be identified and possible surgical interventions can be tested on the model before being used on the patient.

To obtain accurate guiding information, these models must be extremely detailed, requiring the use of large HPC systems. The current state-of-the-art software requires a number of hours on such systems to simulate a single beat of a human heart. Computational studies of arrhythmias require many hundreds of beats and so the current performance is not yet good enough to provide useful surgical data.

The most efficient software package available for heart modelling is the Cardiac Arrhythmia Research Package (CARP). Recently, EPCC has been working with Dr Gernot Plank and the OeRC, lead developers of CARP, to identify performance problems in the code and suggest how they should be addressed. A two-month study, conducted as part of DEISA Extreme Computing Initiative project muHeart, identified three main areas of interest.

Preliminary work addressing these areas suggests that eliminating the identified performance issues could reduce the time required for heart beat simulations from hours to minutes. This is an exciting development, since it brings the prospect of using computational models as part of the surgical workflow very much closer.

Dr Plank said: "The profiling work EPCC has carried out has been extremely important in guiding plans for future model development and I am very much looking forward to continuing the work to extend these results to performance improvements. The performance improvements will enable us to simulate the electrical activity of the heart in health and under pathological conditions at an unprecedented level of anatomical and functional detail which will, eventually, pave the way to personalised medicine."

The funding to carry out the performance optimisation was awarded to EPCC and Dr Gernot Plank through the dCSE programme. The work will be carried out on HECToR during 2010.

The dCSE awards are designed to either improve existing applications on HECToR or enable codes for use on HECToR by funding specialist software help. EPCC is available for collaboration in proposal generation and providing technical effort and expertise to perform the project work. Further information is available at http://www.epcc.ed.ac.uk/research-collaborations/hector-dcse.

-----

Source: The University of Edinburgh

Article Tools

Share Options

(Digg, Technorati, more)

Subscribe

Subscribe to HPCwire

Discussion

There are 0 discussion items posted.

RSS Feeds

Feeds by Topic

Feeds by Industry

Feeds by Content Type

Feature Articles

SDSC Puts Data at Center Stage

The naming of Michael Norman as director of the San Diego Supercomputer Center (SDSC) last week was long overdue. SDSC has been without an official director for more than 14 months, with Norman filling the spot as the interim head since last July. The appointment could mark something of a comeback for the center, which has not only gone director-less during this time, but has been operating without a high-end supercomputer as well.
Read More...

The Week in Review

The National Science Foundation has awarded funding to four projects as part of the Future Internet Architecture program; and the 3PAR bidding war is won by HP. We recap those stories and more in our weekly wrapup.
Read More...

Intel Flexes Parallel Programming Muscles

Intel Corp has released Parallel Studio 2011, a set of four tools designed to mainstream software development on multicore x86 architectures. The update folds in a number of parallel programming technologies that the company has acquired or developed independently over the past few years, including the Cilk Arts and RapidMind technologies, and Intel's own Ct data parallel language framework.
Read More...

Read more HPCwire features...

Around the Web

The Mainstreaming of HPC

Sep 08 | Closing the gap between HPC and mainstream IT. Read more...

Data Mined for Love Connection

Sep 07 | Clues left on social media sites help singles find love. Read more...

Picking the Right Processor

Sep 03 | Should engineers take advantage of GPU computing? Read more...

HP, Hynix Start Memristor on Path to Commercialization

Sep 02 | Could see first products in three years. Read more...

TED Talks for the IT Crowd

Sep 01 | A hand-picked selection of video presentations from the TED conference -- because the next big thing has to start somewhere. Read more...

Read more headlines...

Featured Whitepapers

Breaking Through Real World Storage Barriers in Next Generation Sequencing

Jul 20 | | BlueArc's network storage systems are compelling solutions for the evolving and unpredictable needs of an NGS environment. They offer significant performance, scalability, utilization and cost benefits, while catering to the manageability needs of various users in a research organization.

Effective Backup and Restore

Jul 29 | | Panasas storage solutions deliver high throughput with many concurrent backup IO streams to standard backup applications such as Veritas NetBackup™ or EMC® NetWorker™. Download this whitepaper to understand the essential elements for effective backup and restore: the tape subsystem, networking, file system workload and administrative policy.

View the White Paper Library

Multimedia

Webcast: Are you drowning in data?

In this webinar you will hear about the current storage challenges facing the HPC community, how Panasas storage solutions provide exceptional performance, scalability, and manageability, and how you can achieve the lowest total Cost of Ownership with a system that installs and configures in 15 minutes.

Webcast: Virtualized Data Center Roundtable

Join this online panel discussion for live Q&A with leading industry experts, analysts, and end-users to discuss the latest innovations, best practices, barriers to implementation, and measurable benefits of server virtualization with a particular focus on today's real world solutions.

Webcast: Watch SC09 Birds of a Feather Video: Scalable Fault-Tolerant HPC Supercomputers

Learn about scalable fault-tolerant architectures and examples of energy efficient and scalable supercomputing clusters using dual QDR InfiniBand to combine capacity computing with network failover capabilities with the help of programming languages such as MPI and a robust Linux cluster management package.