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Original Research Article
PyNEST: A convenient interface to the NEST simulator

1  Bernstein Center for Computational Neuroscience, Albert-Ludwigs-University, Germany
2  Honda Research Institute Europe GmbH, Germany
3  Laboratory for Computational Neuroscience, Swiss Federal Institute of Technology, EPFL, Switzerland
4  Theoretical Neuroscience Group, Riken Brain Science Institute, Japan
5  Computational Science Research Program, RIKEN, Japan


The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10^4 neurons and 10^7 to 10^9 synapses. NEST is implemented in C++ and can be used on a large range of architectures from single-core laptops over multi-core desktop computers to super-computers with thousands of processor cores. Python (http://www.python.org) is a modern programming language that has recently received considerable attention in Computational Neuroscience. Python is easy to learn and has many extension modules for scientific computing (e.g. http://www.scipy.org). In this contribution we describe PyNEST, the new user interface to NEST. PyNEST combines NEST’s efficient simulation kernel with the simplicity and flexibility of Python. Compared to NEST’s native simulation language SLI, PyNEST makes it easier to set up simulations, generate stimuli, and analyze simulation results. We describe how PyNEST connects NEST and Python and how it is implemented. With a number of examples, we illustrate how it is used.

Keywords: Python, modelling, integrate-and-fire neuron, large-scale simulation, scientific computing, Networks, programming

Citation: Eppler JM, Helias M, Muller E, Diesmann M and Gewaltig M (2008) PyNEST: A convenient interface to the NEST simulator. Front. Neuroinform. doi:10.3389/neuro.11.012.2008

Received: 14 September 2008; paper pending published: 29 September 2008; accepted: 30 December 2008;

Edited by: 
Rolf Kötter, Radboud University Nijmegen, The Netherlands

Reviewed by: 
Upinder S. Bhalla, National Center for Biological Sciences, India

Copyright: © Eppler, Helias, Muller, Diesmann and Gewaltig. 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: Jochen Martin Eppler, Honda Research Institute Europe GmbH, Carl-Legien-Str. 30, 63073 Offenbach am Main, Germany. eppler@biologie.uni-freiburg.de

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