Back to Table of contents

Primeur weekly 2014-06-30

Special

Innovative HTC facilities needed to support computational genomics at the application and data level ...

HPC-assisted cell-based immunotherapy successful in curing melanoma ...

Restless hearts are simulated with real-time modelling at IBM Research in Zurich ...

A live report from the Adapteva A-1 "smallest supercomputer in the world" launch at ISC'14 ...

The Cloud

HP launches Helion Managed Services for optimizing Cloud storage workloads ...

Oracle unveils next generation Virtual Compute Appliance ...

Desktop Grids

ATLAS@Home crowd computing project launched at CERN ...

EuroFlash

a.s.r. uses ADVA Optical Networking's GNOC for critical network monitoring and maintenance ...

ADVA Optical Networking launches new era of data centre connectivity with Big Data transport solution ...

KTH wins from crystal clear insight into application performance with Allinea Performance Reports ...

Neurological simulation milestone reached after UCL embraces Allinea's tools on UK's largest supercomputer ...

Bright Computing is building on its success in data centres across Europe ...

UK Atomic Weapons Establishment launches SGI supercomputer ...

Spectra Logic tape library to archive the UK's fastest supercomputer ...

Physicists find way to boot up quantum computers 72 times faster than previously possible ...

In the fast lane: Mediatec uses Calibre UK LEDView530 scalers at FIA World Endurance Championships ...

The upcoming cybernetic age is one of intellectual capital ...

International Supercomputing Conference moves to Frankfurt, Germany in 2015 ...

USFlash

DataDirect Networks helps EMSL speed climate, energy and bioscience discoveries with high performance and massively scalable storage ...

Spectra and the Tandy Supercomputer shorten calculation rates from days to minutes, saving time and lives ...

New A*STAR-SMU centre combines high-powered computing and behavioural sciences to study people-centric issues ...

Scheduling algorithms based on game theory makes better use of computational resources ...

National Renewable Energy Laboratory supercomputer tackles power grid problems ...

Simulations helps scientists understand and control turbulence in humans and machines ...

Stampede supercomputer enables discoveries throughout science and engineering ...

Supercomputing simulations crucial to the study of Ras protein in determining anticancer drugs ...

Stampede supercomputer powers innovations in DNA sequencing technologies ...

Stampede supercomputer helps researchers design and test improved hurricane forecasting system ...

NSF-supported Stampede supercomputer powers innovations in materials science ...

D-Wave and predecessors: From simulated to quantum annealing ...

HPC server market shrinks -9.6% in the first quarter of 2014, according to IDC ...

University of Maryland's Deepthought2 debuts in global supercomputer rankings ...

Nine ways NSF-supported supercomputers help scientists understand and treat the disease ...

CAST releases wysiwyg R33 ...

Restless hearts are simulated with real-time modelling at IBM Research in Zurich


24 Jun 2014 Leipzig - In the session on HPC in Life Sciences at ISC'14 in Leipzig, Matthias Reumann from IBM Zurich, talked about the simulation of drug-induced arrhythmias. HPC is used in this cardiologic area to perform real-time modelling of human heart ventricles at a cellular resolution.

Sudden cardiac arrest is the leading cause of death, stated Matthias Reumann. In the USA, there are about 424,000 deaths per year due to cardiac arrest. That is one casualty every 1 minute and 15 seconds. Globally, there are 6.3 million deaths per year which is one every 5 seconds.

The bad news is that drugs can promote arrhythmia and SCA, and can even cause anti-arrhytmics. These irregular and chaotic electrical disturbances in the heart cause a lot of reason to worry.

Matthias Reumann explained the anatomy and electrophysiology of arrythmia. The heart pumps blood through the body with electrical activity. The ions are moving across the cells.

There is a multi-scale reaction for the diffusion of cardiac models with non-linear stiff ODEs. The 3 to 100 state variables per cell are depending on the model's detail. We are talking about 370 million of tissue cells, stated Matthias Reumann.

Matthias Reumann started in 2007 to model electrophysiology in the heart. One single heartbeat would cost 2 weeks to simulate. Cardioid however is 1200 times faster than the state-of-the-art software, he told the audience with 58,8% of peak performance on the full Sequoia, which amounts to about 1,6 million cores.

Matthias Reumann expanded on the Big Data challenge that we are facing. When researchers are just looking at l/m - 8 bytes (double precision) with 0.05 mm resolution, 3 billion elements are involved, costing 1 petaByte per 1 minute simulation.

A single cell means 1 byte and 1 minute simulation. In basic science, we are talking 8x1x60,000, meaning 48 kiloByte per 1 minute simulation, stated Matthias Reumann.

For the experimental ventricular wedge preparation, methods involve the construction of a 1-D cable. The in silico model is an independent risk factor. Predictive modelling involves risk assessment.

Predictive modelling on drug effects is amounting to 8 x 200 x 200 x 200 x 60,000, calculated Matthias Reumann. Are those wedges predictive for the whole heart? In fact, the heart has very fine structures. It is not clear how the distribution of these structures is, explained Matthias Reumann.

For the predictive modelling of the whole heart, scientists require 0,05 mm resolution, meaning 1 petaByte.

A 0,1 mm resolution amounts to 0.1 Petabyte.

Matthias Reumann presented a number of open questions to the audience:

  • When reducing the spatial resolution by factor 10-25, are the simulations accurately predictive?
  • When reducing the temporal resolution by factor 5, are the simulations still accurately predictive?
  • When reducing the data accuracy by factor 8, is there a loss of information?
  • When reducing the wedge simulation by 2 orders of magnitude, are the simulations still accurately predictive?
  • When reducing the run time of the visualization, is there a loss of all information?

Matthias Reumann showed the example of a simulation of E-4031 and Ranolazine with the S1-S2 protocol.

The Genome Wide Association Studies (GWAS) are being used to identify common genetic factors that influence health and disease. Is a single gene related to a phenotypic trait? Researchers use an univariate analysis.

The bottleneck is the computation time, explained Matthias Reumann.

A study with 1 million SNPs has 500 billion SNP pairs or 1667 trillion SNP triplets. Increasingly large datasets cannot be stored in the memory.

Is a single gene related to a phenotypic trait? Gene-gene and gene-environment interactions are computationally expensive. There are about 10 million single nucleotide polymorphisms in the human genome.

The results include a two-way interaction of 2000 samples of 1.1 million SNPs, computed in about 12 minutes, stated Matthias Reumann.

What if the researchers find something new? The GWAS depth analysis is being performed. There are SNPs in about 40 candidate genes.

Computational, data driven analytics involves machine learning, interpretation, data extraction, exploration, and cataloguing.

The domain knowledge includes spatial modelling of cellular processes and the whole cell. The problem, according to Matthias Reumann, is which impact does the cell shape have? This is described in a paper titled "The dawn of Virtual Cell Biology".

Simulating the cell is performed with network dynamics showing differential equations on a simulation time scale.

The molecular dynamics simulation is based on first principles, stated Matthias Reumann. The time scale amounts to just micro seconds which is not sufficient.

Matthias Reumann concluded by saying that Big Data and analytics are enormous challenges in the life sciences. Researchers still have a lot of thinking to do.
Leslie Versweyveld

Back to Table of contents

Primeur weekly 2014-06-30

Special

Innovative HTC facilities needed to support computational genomics at the application and data level ...

HPC-assisted cell-based immunotherapy successful in curing melanoma ...

Restless hearts are simulated with real-time modelling at IBM Research in Zurich ...

A live report from the Adapteva A-1 "smallest supercomputer in the world" launch at ISC'14 ...

The Cloud

HP launches Helion Managed Services for optimizing Cloud storage workloads ...

Oracle unveils next generation Virtual Compute Appliance ...

Desktop Grids

ATLAS@Home crowd computing project launched at CERN ...

EuroFlash

a.s.r. uses ADVA Optical Networking's GNOC for critical network monitoring and maintenance ...

ADVA Optical Networking launches new era of data centre connectivity with Big Data transport solution ...

KTH wins from crystal clear insight into application performance with Allinea Performance Reports ...

Neurological simulation milestone reached after UCL embraces Allinea's tools on UK's largest supercomputer ...

Bright Computing is building on its success in data centres across Europe ...

UK Atomic Weapons Establishment launches SGI supercomputer ...

Spectra Logic tape library to archive the UK's fastest supercomputer ...

Physicists find way to boot up quantum computers 72 times faster than previously possible ...

In the fast lane: Mediatec uses Calibre UK LEDView530 scalers at FIA World Endurance Championships ...

The upcoming cybernetic age is one of intellectual capital ...

International Supercomputing Conference moves to Frankfurt, Germany in 2015 ...

USFlash

DataDirect Networks helps EMSL speed climate, energy and bioscience discoveries with high performance and massively scalable storage ...

Spectra and the Tandy Supercomputer shorten calculation rates from days to minutes, saving time and lives ...

New A*STAR-SMU centre combines high-powered computing and behavioural sciences to study people-centric issues ...

Scheduling algorithms based on game theory makes better use of computational resources ...

National Renewable Energy Laboratory supercomputer tackles power grid problems ...

Simulations helps scientists understand and control turbulence in humans and machines ...

Stampede supercomputer enables discoveries throughout science and engineering ...

Supercomputing simulations crucial to the study of Ras protein in determining anticancer drugs ...

Stampede supercomputer powers innovations in DNA sequencing technologies ...

Stampede supercomputer helps researchers design and test improved hurricane forecasting system ...

NSF-supported Stampede supercomputer powers innovations in materials science ...

D-Wave and predecessors: From simulated to quantum annealing ...

HPC server market shrinks -9.6% in the first quarter of 2014, according to IDC ...

University of Maryland's Deepthought2 debuts in global supercomputer rankings ...

Nine ways NSF-supported supercomputers help scientists understand and treat the disease ...

CAST releases wysiwyg R33 ...