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Original Research ARTICLE

A component-based extension framework for large-scale parallel simulations in NEURON

James G. King¹, Michael Hines², Sean Hill¹, Philip H. Goodman³, Henry Markram¹ and Felix Schürmann^1*

Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

Department of Computer Science, Yale University, New Haven, CT, USA

Department of Medicine and Program in Biomedical Engineering, University of Nevada, Reno, NV, USA

As neuronal simulations approach larger scales with increasing levels of detail, the neurosimulator software represents only a part of a chain of tools ranging from setup, simulation, interaction with virtual environments to analysis and visualizations. Previously published approaches to abstracting simulator engines have not received wide-spread acceptance, which in part may be to the fact that they tried to address the challenge of solving the model specification problem. Here, we present an approach that uses a neurosimulator, in this case NEURON, to describe and instantiate the network model in the simulator’s native model language but then replaces the main integration loop with its own. Existing parallel network models are easily adopted to run in the presented framework. The presented approach is thus an extension to NEURON but uses a component-based architecture to allow for replaceable spike exchange components and pluggable components for monitoring, analysis, or control that can run in this framework alongside with the simulation.

Keywords:

large-scale simulation, NEURON simulator, parallel, distributed

Citation:

King JG, Hines M, Hill S, Goodman PH, Markram H and Schürmann F (2009). A component-based extension framework for large-scale parallel simulations in NEURON. Front. Neuroinform. 3:10. doi: 10.3389/neuro.11.010.2009

Received:

10 December 2008;

Paper pending published:

18 December 2008;

Accepted:

08 April 2009;

Published online:

27 April 2009.

Edited by:

Erik De Schutter, University of Antwerp, Belgium; Okinawa Institute of Science and Technology, Japan

Reviewed by:

Robert C. Cannon, Textensor Limited, UK
Hugo Cornelis, University of Texas Health Science Center at San Antonio, USA

© 2009 King, Hines, Hill, Goodman, Markram and Schürmann. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.

*Correspondence:

Felix Schürmann, Brain Mind Institute, EPFL, AA/AA-VP/BBP Station 15, 1015 Lausanne, Switzerland. e-mail: felix.schuermann@epfl.ch