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This article is part of the Research Topic Python in Neuroscience II

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Front. Neuroinform., 11 April 2014 | http://dx.doi.org/10.3389/fninf.2014.00037

Python-based geometry preparation and simulation visualization toolkits for STEPS

  • Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Okinawa, Japan

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations.

Keywords: STEPS, stochastic reaction diffusion simulation, Python, geometry preparation, simulation visualization, tetrahedral mesh, Stochastic Simulation Algorithm

Citation: Chen W and De Schutter E (2014) Python-based geometry preparation and simulation visualization toolkits for STEPS. Front. Neuroinform. 8:37. doi: 10.3389/fninf.2014.00037

Received: 24 October 2013; Accepted: 25 March 2014;
Published online: 11 April 2014.

Edited by:

Eilif Benjamin Muller, École Polytechnique Fédérale de Lausanne, Switzerland

Reviewed by:

Jeanette Hellgren Kotaleski, Karolinska Institute, Sweden
Daniel Keller, École Polytechnique Fédérale de Lausanne, Switzerland

Copyright © 2014 Chen and De Schutter. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Weiliang Chen, Computational Neuroscience Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami, Okinawa, 904-0495, Japan e-mail: w.chen@oist.jp