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PyMOOSE: Interoperable scripting in Python for MOOSE

Upinder S. Bhalla
2008 Frontiers in Neuroinformatics  
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 illustrate this by using Python numerical libraries to analyze MOOSE output online, and by developing a GUI in Python/Qt for a MOOSE simulation.  ...  Ray to attend the FACETS/CodeJam meeting at CNRS, Gif-sur-Yvette, which further stimulated PyMOOSE development.  ... 
doi:10.3389/neuro.11.006.2008 pmid:19129924 pmcid:PMC2614320 fatcat:aigohyiverejrkutfi7d4nexlm

Time to Bring Single Neuron Modeling into 3D

Weiliang Chen, Erik De Schutter
2017 Neuroinformatics  
, 4 etc., is based on mathematical methods developed in the 50s and 60s, before supercomputers were available for scientific research.  ...  reasonable detail, the underlying equations ignore many 3D aspects by computing the changes in membrane potential in a branched 1D cable.  ...  PyMOOSE: interoperable scripting in Python for MOOSE. Frontiers in Neuroinformatics, 2, 6. 5 Rall, W. (1959). Branching dendritic trees and motoneuron membrane resistivity.  ... 
doi:10.1007/s12021-016-9321-x pmid:28058618 fatcat:puxlalg6jjdzjo4u5neldkum7u

PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python

Dejan Pecevski
2009 Frontiers in Neuroinformatics  
The API of the PCSIM library is exposed to the Python programming language by means of the Python extension module pypcsim (see Sec. 3 for details).  ...  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  ...  Davison for helpful discussions.  ... 
doi:10.3389/neuro.11.011.2009 pmid:19543450 pmcid:PMC2698777 fatcat:7xniocmkyfclljxc2qiolrr27q

CyNEST: a maintainable Cython-based interface for the NEST simulator

Yury V. Zaytsev, Abigail Morrison
2014 Frontiers in Neuroinformatics  
We are deeply grateful to the Cython community for their support throughout the project, and in particular to Stefan Behnel, Robert Bradshaw, Sturla Molden, and Nikita Nemkin.  ...  We warmly thank the NEST Initiative, in particular Jochen Martin Eppler, Hans Ekkehard Plesser, Markus Diesmann, and Marc-Oliver Gewaltig, for their support and constructive discussions.  ...  The former is exploited in PyMOOSE (Ray and Bhalla, 2008) , the Python interface to the MOOSE simulator, while the latter is used in PCSIM (Pecevski et al., 2009) in conjunction with the Boost.Python  ... 
doi:10.3389/fninf.2014.00023 pmid:24672470 pmcid:PMC3953856 fatcat:pm77zgj27nawratv6juopdu7sm

A Federated Design for a Neurobiological Simulation Engine: The CBI Federated Software Architecture

Hugo Cornelis, Allan D. Coop, James M. Bower, Kelvin E. Jones
2012 PLoS ONE  
Simulator interoperability and extensibility has become a growing requirement in computational biology. To address this, we have developed a federated software architecture.  ...  The software architecture we describe here allows for both these approaches.  ...  Acknowledgments We thank the Computational Biology Initiative at UTSA (http://www.cbi. utsa.edu) for their support when installing, using, and updating G-3 on their computers.  ... 
doi:10.1371/journal.pone.0028956 pmid:22242154 pmcid:PMC3252298 fatcat:h6ktjjuuengqjo4ew3ymtepr2y