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Original Research ARTICLE

This article is part of a Research Topic

PyMOOSE: interoperable scripting in Python for MOOSE

National Centre for Biological Sciences, Bangalore, India

Python is emerging as a common scripting language for simulators. This opens up many possibilities for interoperability in the form of analysis, interfaces, and communications between simulators. We report the integration of Python scripting with the Multi-scale Object Oriented Simulation Environment (MOOSE). MOOSE is a general-purpose simulation system for compartmental neuronal models and for models of signaling pathways based on chemical kinetics. We show how the Python-scripting version of MOOSE, PyMOOSE, combines the power of a compiled simulator with the versatility and ease of use of Python. We illustrate this by using Python numerical libraries to analyze MOOSE output online, and by developing a GUI in Python/Qt for a MOOSE simulation. Finally, we build and run a composite neuronal/signaling model that uses both the NEURON and MOOSE numerical engines, and Python as a bridge between the two. Thus PyMOOSE has a high degree of interoperability with analysis routines, with graphical toolkits, and with other simulators.

Keywords:

simulators, compartmental models, systems biology, NEURON, GENESIS, multi-scale models, Python, MOOSE

Citation:

Ray S and Bhalla US (2008). PyMOOSE: interoperable scripting in Python for MOOSE. Front. Neuroinform. 2:6. doi: 10.3389/neuro.11.006.2008

Received:

15 September 2008;

Paper pending published:

13 October 2008;

Accepted:

01 November 2008;

Published online:

19 December 2008.

Edited by:

Rolf Kötter, Radboud University Nijmegen, Netherlands

Reviewed by:

Michael Hines, Yale University, USA
Hugo Cornelis, UTHSCSA, USA

© 2008 Ray and Bhalla. 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:

Upinder S. Bhalla, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India. e-mail: bhalla@ncbs.res.in