A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
PyMOOSE: Interoperable scripting in Python for MOOSE
2008
Frontiers in Neuroinformatics
Preserved Fulltext
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
2017
Neuroinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
, 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
2009
Frontiers in Neuroinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2014
Frontiers in Neuroinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2012
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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