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BrainFrame

Automated framework for rapid simulations of high-detail brain models

Total Cost €

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EC-Contrib. €

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Partnership

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Project "BrainFrame" data sheet

The following table provides information about the project.

Coordinator
ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM 

Organization address
address: DR MOLEWATERPLEIN 40
city: ROTTERDAM
postcode: 3015 GD
website: www.erasmusmc.nl

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Total cost 149˙937 €
 EC max contribution 149˙937 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-PoC
 Funding Scheme ERC-POC
 Starting year 2015
 Duration (year-month-day) from 2015-02-01   to  2016-01-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM NL (ROTTERDAM) coordinator 149˙937.00

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 Project objective

Traditional methods of software modeling and simulation take prohibitive amounts of time to run for the size and complexity of biologically realistic neuron populations (e.g. >1 million). For instance, simulation of a 100 high-detail (Inferior-Olive) neuron-network for 10 minutes of brain time take 42 hours to complete on an modern PC workstation. To tackle this problem - common to the international neuroscience community -, we have turned to hardware-accelerated simulation platforms. We have employed award-winning, FPGA -based, dataflow machines provided by Maxeler Technologies, which offer high-performance computing capabilities and come with programming tools of unprecedented user friendliness. Our current Maxeler setups have offered impressive acceleration rates of more than 4 orders of magnitude (x10000). Despite the achieved speeds, however, we have found the Maxeler programming tools to be cumbersome to learn by neuromodelers with little hardware knowledge. Engineering personnel has, thus, been employed to assist them in (efficiently) translating and deploying their models. To streamline this process and bring a powerful tool directly to the hands of modelers, we propose BrainFrame, a novel system consisting of Maxeler hardware and a comprehensive software toolflow, effectively adding an abstraction level for neuromodelers to work on without specific knowledge of the underlying simulation platform. BrainFrame comprises a “one-stop shop”, integrated solution primarily targeting labs and companies active in the field of brain-modeling research and applications.

 Publications

year authors and title journal last update
List of publications.
2016 G. Chatzikonstantis, D. Rodopoulos, S. Nomikou, C. Strydis, C. I. De Zeeuw and D. Soudris
First Impressions from Detailed Brain Model Simulations on a Xeon-Xeon Phi Node
published pages: , ISSN: , DOI:
ACM International Conference on Computing Frontiers 2016 2019-07-22
2015 Lieke Kros, Oscar H. J. Eelkman Rooda, Jochen K. Spanke, Parimala Alva, Marijn N. van Dongen, Athanasios Karapatis, Else A. Tolner, Christos Strydis, Neil Davey, Beerend H. J. Winkelman, Mario Negrello, Wouter A. Serdijn, Volker Steuber, Arn M. J. M. van den Maagdenberg, Chris I. De Zeeuw, Freek E. Hoebeek
Cerebellar output controls generalized spike-and-wave discharge occurrence
published pages: 1027-1049, ISSN: 0364-5134, DOI: 10.1002/ana.24399
Annals of Neurology 77/6 2019-07-22
2015 Lieke Kros, Oscar H.J. Eelkman Rooda, Chris I. De Zeeuw, Freek E. Hoebeek
Controlling Cerebellar Output to Treat Refractory Epilepsy
published pages: 787-799, ISSN: 0166-2236, DOI: 10.1016/j.tins.2015.10.002
Trends in Neurosciences 38/12 2019-07-22
2016 G. Smaragdos, G. Chatzikostantis, S. Nomikou, D. Rodopoulos, I. Sourdis, D. Soudris, C. I. De Zeeuw and C. Strydis
Performance Analysis of Accelerated Biophysically-Meaningful Neuron Simulations
published pages: , ISSN: , DOI:
IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS) 2016 2019-07-22
2016 H.A. Du Nguyen, Z. Al-Ars, G. Smaragdos, C. Strydis
Accelerating complex brain-model simulations on GPU platforms
published pages: , ISSN: , DOI:
Design, Automation, and Test in Europe, DATE 2015 2019-07-22

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