Literature DB >> 19198661

NEURON and Python.

Michael L Hines1, Andrew P Davison, Eilif Muller.   

Abstract

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications.

Entities:  

Keywords:  Python; computational neuroscience; simulation environment

Year:  2009        PMID: 19198661      PMCID: PMC2636686          DOI: 10.3389/neuro.11.001.2009

Source DB:  PubMed          Journal:  Front Neuroinform        ISSN: 1662-5196            Impact factor:   4.081


  6 in total

Review 1.  Expanding NEURON's repertoire of mechanisms with NMODL.

Authors:  M L Hines; N T Carnevale
Journal:  Neural Comput       Date:  2000-05       Impact factor: 2.026

Review 2.  Towards NeuroML: model description methods for collaborative modelling in neuroscience.

Authors:  N H Goddard; M Hucka; F Howell; H Cornelis; K Shankar; D Beeman
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2001-08-29       Impact factor: 6.237

3.  Parallel network simulations with NEURON.

Authors:  M Migliore; C Cannia; W W Lytton; Henry Markram; M L Hines
Journal:  J Comput Neurosci       Date:  2006-05-26       Impact factor: 1.621

4.  Translating network models to parallel hardware in NEURON.

Authors:  M L Hines; N T Carnevale
Journal:  J Neurosci Methods       Date:  2007-09-16       Impact factor: 2.390

5.  Fully implicit parallel simulation of single neurons.

Authors:  Michael L Hines; Henry Markram; Felix Schürmann
Journal:  J Comput Neurosci       Date:  2008-04-01       Impact factor: 1.621

Review 6.  MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification.

Authors:  Sharon Crook; Padraig Gleeson; Fred Howell; Joseph Svitak; R Angus Silver
Journal:  Neuroinformatics       Date:  2007
  6 in total
  130 in total

1.  Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow.

Authors:  David B Stockton; Fidel Santamaria
Journal:  Neuroinformatics       Date:  2017-10

2.  Intrinsic dendritic filtering gives low-pass power spectra of local field potentials.

Authors:  Henrik Lindén; Klas H Pettersen; Gaute T Einevoll
Journal:  J Comput Neurosci       Date:  2010-05-26       Impact factor: 1.621

3.  Ketamine disrupts θ modulation of γ in a computer model of hippocampus.

Authors:  Samuel A Neymotin; Maciej T Lazarewicz; Mohamed Sherif; Diego Contreras; Leif H Finkel; William W Lytton
Journal:  J Neurosci       Date:  2011-08-10       Impact factor: 6.167

4.  Synchronous Infra-Slow Bursting in the Mouse Accessory Olfactory Bulb Emerge from Interplay between Intrinsic Neuronal Dynamics and Network Connectivity.

Authors:  Asaph Zylbertal; Yosef Yarom; Shlomo Wagner
Journal:  J Neurosci       Date:  2017-02-01       Impact factor: 6.167

5.  Inhibitory suppression of heterogeneously tuned excitation enhances spatial coding in CA1 place cells.

Authors:  Christine Grienberger; Aaron D Milstein; Katie C Bittner; Sandro Romani; Jeffrey C Magee
Journal:  Nat Neurosci       Date:  2017-01-23       Impact factor: 24.884

6.  Persistent Sodium Current Mediates the Steep Voltage Dependence of Spatial Coding in Hippocampal Pyramidal Neurons.

Authors:  Ching-Lung Hsu; Xinyu Zhao; Aaron D Milstein; Nelson Spruston
Journal:  Neuron       Date:  2018-06-14       Impact factor: 17.173

7.  Establishing a novel modeling tool: a python-based interface for a neuromorphic hardware system.

Authors:  Daniel Brüderle; Eric Müller; Andrew Davison; Eilif Muller; Johannes Schemmel; Karlheinz Meier
Journal:  Front Neuroinform       Date:  2009-06-05       Impact factor: 4.081

8.  Trends in programming languages for neuroscience simulations.

Authors:  Andrew P Davison; Michael L Hines; Eilif Muller
Journal:  Front Neurosci       Date:  2009-12-15       Impact factor: 4.677

9.  The brian simulator.

Authors:  Dan F M Goodman; Romain Brette
Journal:  Front Neurosci       Date:  2009-09-15       Impact factor: 4.677

10.  [Not Available].

Authors:  Dejan Pecevski; Thomas Natschläger; Klaus Schuch
Journal:  Front Neuroinform       Date:  2009-05-27       Impact factor: 4.081

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