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Original Research ARTICLE

This article is part of a Research Topic

PCSIM: a parallel simulation environment for neural circuits fully integrated with Python

Dejan Pecevski^1*, Thomas Natschläger² and Klaus Schuch¹

Institute for Theoretical Computer Science, Graz University of Technology, Graz, Austria

Software Competence Center Hagenberg, Hagenberg, Austria

The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM’s primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM’s full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM’s object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM’s functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations.

Keywords:

neural simulator, parallel simulation, spiking neurons, Python, Boost.Python, Py++, PCSIM

Citation:

Pecevski D, Natschläger T and Schuch K (2009). PCSIM: a parallel simulation environment for neural circuits fully integrated with Python. Front. Neuroinform. 3:11. doi: 10.3389/neuro.11.011.2009

Received:

14 September 2008;

Paper pending published:

21 October 2008;

Accepted:

21 April 2009;

Published online:

27 May 2009.

Edited by:

Rolf Kötter, Radboud University Nijmegen, The Netherlands

Reviewed by:

Ingo Bojak, Radboud University Nijmegen, The Netherlands
Abigail Morrison, RIKEN, Japan

© 2009 Pecevski, Natschläger and Schuch. 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:

Dejan Pecevski, Institute for Theoretical Computer Science, Graz University of Technology, Inffeldgasse 16b/1, A-8010 Graz, Austria. e-mail: dejan@igi.tugraz.at