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Primeur weekly 2017-03-27

Focus

Primeur Live! about the EuroHPC annnouncement on European Exascale agreement ...

Focus on Europe

Molecular motor-powered biocomputers ...

PRACE 2: growth in capacity for growth in excellence ...

"Piz Daint" for Europe, European supercomputers for Switzerland ...

Relocation of Paris PoP brings new opportunities for international collaboration ...

ISC High Performance adds STEM Student Day to the 2017 programme ...

The eScience Center and NWO-Shell join forces for future energy ...

Digital revolution needs generosity to cope with citizens' life-changing challenges - Investment in research and innovative HPC, exascale and quantum technologies is key ...

Middleware

Canada funds $125 million Pan-Canadian Artificial Intelligence Strategy ...

e-IRG support project to organise BOF session on Data Infrastructure Assessment at RDA 9th Plenary ...

Hardware

Method speeds testing of new networking protocols ...

Asperitas revealed their first sustainable liquid cooled modular data centre solution ...

DDN names Bret Costelow VP of Global Sales ...

Mellanox introduces new 100Gb/s silicon photonics optical engine product line ...

Mellanox doubles silicon photonics Ethernet transceiver speeds to 200Gb/s ...

Applications

Deep learning and stock trading ...

Parallel computation provides deeper insight into brain function ...

Machine learning lets scientists reverse-engineer cellular control networks ...

Research results in AI for drug discovery to be presented at the BioDataWorld West in San Francisco ...

Breaking the supermassive black hole speed limit ...

When helium behaves like a black hole ...

A robust, two-ion quantum logic gate that operates in a microsecond is designed ...

Big Data approach to predict protein structure ...

Molecular treasure maps to help discover new materials ...

Scientists use IBM Power systems to assemble genome of West Nile mosquito ...

Young talents challenge the world's fastest supercomputer and AI applications ...

Interpretable machine learning for all at Duke University ...

Ohio Supercomputer Center Workshops highlight resources ...

NASA's hybrid computer enables Raven's autonomous rendez-vous capability ...

The Cloud

Precision medicine platform now open for collaborative discovery about cardiovascular diseases ...

IBM automates compliance controls and data security for multi-Cloud workloads ...

Oracle Cloud Platform continues to gain momentum with customers, partners, and developers ...

IBM launches Bluemix Container Service with Kubernetes to fuel highly secure and rapid development of cognitive apps ...

Oracle Health Sciences Data Management Workbench now available in the Cloud ...

Veritas and IBM join forces to drive data management further in the Cloud ...

Parallel computation provides deeper insight into brain function


By breaking the partial Purkinje cell model (A) down into 50 sections (B-top) or 1000 sections (B-bottom) and running computations of each section in parallel on a supercomputer, OIST researchers dramatically reduced the simulation time of the model. Credit: OIST.
23 Mar 2017 Okinawa - Unlike experimental neuroscientists who deal with real-life neurons, computational neuroscientists use model simulations to investigate how the brain functions. While many computational neuroscientists use simplified mathematical models of neurons, researchers in the Computational Neuroscience Unit at the Okinawa Institute of Science and Technology Graduate University (OIST) develop software that models neurons to the detail of molecular interactions with the goal of eliciting new insights into neuronal function. Applications of the software were limited in scope up until now because of the intense computational power required for such detailed neuronal models, but recently Dr. Weiliang Chen, Dr. Iain Hepburn, and Professor Erik De Schutter published two related papers in which they outline the accuracy and scalability of their new high-speed computational software, "Parallel STEPS". The combined findings suggest that Parallel STEPS could be used to reveal new insights into how individual neurons function and communicate with each other.

The first paper, published inThe Journal of Chemical Physicsin August 2016, focuses on ensuring that the accuracy of Parallel STEPS is comparable with conventional methods. In conventional approaches, computations associate with neuronal chemical reactions and molecule diffusion are all calculated on one computational processing unit or 'core' sequentially. However, Dr. Iain Hepburn and colleagues introduced a new approach to perform computations of reaction and diffusion in parallel which can then be distributed over multiple computer cores, whilst maintaining simulation accuracy to a high degree. The key was to develop an original algorithm separated into two parts - one that computed chemical reaction events and the other diffusion events.

"We tested a range of model simulations from simple diffusion models to realistic biological models and found that we could achieve improved performance using a parallel approach with minimal loss of accuracy. This demonstrated the potential suitability of the method on a larger scale", stated Dr. Hepburn.

In a related paper published inFrontiers in Neuroinformaticsthis February, Dr. Weiliang Chen presented the implementation details of Parallel STEPS and investigated its performance and potential applications. By breaking a partial model of a Purkinje cell - one of the largest neurons in the brain - into 50 to 1000 sections and simulating reaction and diffusion events for each section in parallel on the Sango supercomputer at OIST, Dr. Chen and colleagues saw dramatically increased computation speeds. They tested this approach on both simple models and more complicated models of calcium bursts in Purkinje cells and demonstrated that parallel simulation could speed up computations by more than several hundred times that of conventional methods.

"Together, our findings show that Parallel STEPS implementation achieves significant improvements in performance, and good scalability", stated Dr. Chen. "Similar models that previously required months of simulation can now be completed within hours or minutes, meaning that we can develop and simulate more complex models, and learn more about the brain in a shorter amount of time."

Dr. Hepburn and Dr. Chen from OIST's Computational Neuroscience Unit, led by Professor Erik De Schutter, are actively collaborating with the Human Brain Project, a world-wide initiative based at École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland, to develop a more robust version of Parallel STEPS that incorporates electric field simulation of cell membranes.

So far STEPS is only realistically capable of modeling parts of neurons but with the support of Parallel STEPS, the Computational Neuroscience Unit hopes to develop a full-scale model of a whole neuron and subsequently the interactions between neurons in a network. By collaborating with the EPFL team and by making use of the IBM 'Blue Gene/Q' supercomputer located there, they aim to achieve these goals in the near future.

"Thanks to modern supercomputers we can study molecular events within neurons in a much more transparent way than before", stated Prof. De Schutter. "Our research opens up interesting avenues in computational neuroscience that links biochemistry with electrophysiology for the first time."

Source: Okinawa Institute of Science and Technology (OIST) Graduate University

Back to Table of contents

Primeur weekly 2017-03-27

Focus

Primeur Live! about the EuroHPC annnouncement on European Exascale agreement ...

Focus on Europe

Molecular motor-powered biocomputers ...

PRACE 2: growth in capacity for growth in excellence ...

"Piz Daint" for Europe, European supercomputers for Switzerland ...

Relocation of Paris PoP brings new opportunities for international collaboration ...

ISC High Performance adds STEM Student Day to the 2017 programme ...

The eScience Center and NWO-Shell join forces for future energy ...

Digital revolution needs generosity to cope with citizens' life-changing challenges - Investment in research and innovative HPC, exascale and quantum technologies is key ...

Middleware

Canada funds $125 million Pan-Canadian Artificial Intelligence Strategy ...

e-IRG support project to organise BOF session on Data Infrastructure Assessment at RDA 9th Plenary ...

Hardware

Method speeds testing of new networking protocols ...

Asperitas revealed their first sustainable liquid cooled modular data centre solution ...

DDN names Bret Costelow VP of Global Sales ...

Mellanox introduces new 100Gb/s silicon photonics optical engine product line ...

Mellanox doubles silicon photonics Ethernet transceiver speeds to 200Gb/s ...

Applications

Deep learning and stock trading ...

Parallel computation provides deeper insight into brain function ...

Machine learning lets scientists reverse-engineer cellular control networks ...

Research results in AI for drug discovery to be presented at the BioDataWorld West in San Francisco ...

Breaking the supermassive black hole speed limit ...

When helium behaves like a black hole ...

A robust, two-ion quantum logic gate that operates in a microsecond is designed ...

Big Data approach to predict protein structure ...

Molecular treasure maps to help discover new materials ...

Scientists use IBM Power systems to assemble genome of West Nile mosquito ...

Young talents challenge the world's fastest supercomputer and AI applications ...

Interpretable machine learning for all at Duke University ...

Ohio Supercomputer Center Workshops highlight resources ...

NASA's hybrid computer enables Raven's autonomous rendez-vous capability ...

The Cloud

Precision medicine platform now open for collaborative discovery about cardiovascular diseases ...

IBM automates compliance controls and data security for multi-Cloud workloads ...

Oracle Cloud Platform continues to gain momentum with customers, partners, and developers ...

IBM launches Bluemix Container Service with Kubernetes to fuel highly secure and rapid development of cognitive apps ...

Oracle Health Sciences Data Management Workbench now available in the Cloud ...

Veritas and IBM join forces to drive data management further in the Cloud ...