Literature DB >> 20857234

Code generation: a strategy for neural network simulators.

Dan F M Goodman1.   

Abstract

We demonstrate a technique for the design of neural network simulation software, runtime code generation. This technique can be used to give the user complete flexibility in specifying the mathematical model for their simulation in a high level way, along with the speed of code written in a low level language such as C+ +. It can also be used to write code only once but target different hardware platforms, including inexpensive high performance graphics processing units (GPUs). Code generation can be naturally combined with computer algebra systems to provide further simplification and optimisation of the generated code. The technique is quite general and could be applied to any simulation package. We demonstrate it with the 'Brian' simulator ( http://www.briansimulator.org ).

Mesh:

Year:  2010        PMID: 20857234     DOI: 10.1007/s12021-010-9082-x

Source DB:  PubMed          Journal:  Neuroinformatics        ISSN: 1539-2791


  15 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

2.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

3.  Exact subthreshold integration with continuous spike times in discrete-time neural network simulations.

Authors:  Abigail Morrison; Sirko Straube; Hans Ekkehard Plesser; Markus Diesmann
Journal:  Neural Comput       Date:  2007-01       Impact factor: 2.026

Review 4.  Simulation of networks of spiking neurons: a review of tools and strategies.

Authors:  Romain Brette; Michelle Rudolph; Ted Carnevale; Michael Hines; David Beeman; James M Bower; Markus Diesmann; Abigail Morrison; Philip H Goodman; Frederick C Harris; Milind Zirpe; Thomas Natschläger; Dejan Pecevski; Bard Ermentrout; Mikael Djurfeldt; Anders Lansner; Olivier Rochel; Thierry Vieville; Eilif Muller; Andrew P Davison; Sami El Boustani; Alain Destexhe
Journal:  J Comput Neurosci       Date:  2007-07-12       Impact factor: 1.621

Review 5.  CellML and associated tools and techniques.

Authors:  Alan Garny; David P Nickerson; Jonathan Cooper; Rodrigo Weber dos Santos; Andrew K Miller; Steve McKeever; Poul M F Nielsen; Peter J Hunter
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2008-09-13       Impact factor: 4.226

Review 6.  On numerical simulations of integrate-and-fire neural networks.

Authors:  D Hansel; G Mato; C Meunier; L Neltner
Journal:  Neural Comput       Date:  1998-02-15       Impact factor: 2.026

7.  SCoP: an interactive simulation control program for micro- and minicomputers.

Authors:  J M Kootsey; M C Kohn; M D Feezor; G R Mitchell; P R Fletcher
Journal:  Bull Math Biol       Date:  1986       Impact factor: 1.758

8.  An overview of the CellML API and its implementation.

Authors:  Andrew K Miller; Justin Marsh; Adam Reeve; Alan Garny; Randall Britten; Matt Halstead; Jonathan Cooper; David P Nickerson; Poul F Nielsen
Journal:  BMC Bioinformatics       Date:  2010-04-08       Impact factor: 3.169

9.  The brian simulator.

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

10.  Brian: a simulator for spiking neural networks in python.

Authors:  Dan Goodman; Romain Brette
Journal:  Front Neuroinform       Date:  2008-11-18       Impact factor: 4.081

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  15 in total

1.  The connection-set algebra--a novel formalism for the representation of connectivity structure in neuronal network models.

Authors:  Mikael Djurfeldt
Journal:  Neuroinformatics       Date:  2012-07

2.  Brian 2, an intuitive and efficient neural simulator.

Authors:  Romain Brette; Dan Fm Goodman; Marcel Stimberg
Journal:  Elife       Date:  2019-08-20       Impact factor: 8.140

3.  Three tools for the real-time simulation of embodied spiking neural networks using GPUs.

Authors:  Andreas K Fidjeland; David Gamez; Murray P Shanahan; Edgars Lazdins
Journal:  Neuroinformatics       Date:  2013-07

Review 4.  Code Generation in Computational Neuroscience: A Review of Tools and Techniques.

Authors:  Inga Blundell; Romain Brette; Thomas A Cleland; Thomas G Close; Daniel Coca; Andrew P Davison; Sandra Diaz-Pier; Carlos Fernandez Musoles; Padraig Gleeson; Dan F M Goodman; Michael Hines; Michael W Hopkins; Pramod Kumbhar; David R Lester; Bóris Marin; Abigail Morrison; Eric Müller; Thomas Nowotny; Alexander Peyser; Dimitri Plotnikov; Paul Richmond; Andrew Rowley; Bernhard Rumpe; Marcel Stimberg; Alan B Stokes; Adam Tomkins; Guido Trensch; Marmaduke Woodman; Jochen Martin Eppler
Journal:  Front Neuroinform       Date:  2018-11-05       Impact factor: 4.081

Review 5.  Neuronal morphology goes digital: a research hub for cellular and system neuroscience.

Authors:  Ruchi Parekh; Giorgio A Ascoli
Journal:  Neuron       Date:  2013-03-20       Impact factor: 17.173

6.  Democratic population decisions result in robust policy-gradient learning: a parametric study with GPU simulations.

Authors:  Paul Richmond; Lars Buesing; Michele Giugliano; Eleni Vasilaki
Journal:  PLoS One       Date:  2011-05-04       Impact factor: 3.240

7.  Fitting neuron models to spike trains.

Authors:  Cyrille Rossant; Dan F M Goodman; Bertrand Fontaine; Jonathan Platkiewicz; Anna K Magnusson; Romain Brette
Journal:  Front Neurosci       Date:  2011-02-23       Impact factor: 4.677

8.  An efficient simulation environment for modeling large-scale cortical processing.

Authors:  Micah Richert; Jayram Moorkanikara Nageswaran; Nikil Dutt; Jeffrey L Krichmar
Journal:  Front Neuroinform       Date:  2011-09-14       Impact factor: 4.081

9.  The layer-oriented approach to declarative languages for biological modeling.

Authors:  Ivan Raikov; Erik De Schutter
Journal:  PLoS Comput Biol       Date:  2012-05-17       Impact factor: 4.475

10.  ANNarchy: a code generation approach to neural simulations on parallel hardware.

Authors:  Julien Vitay; Helge Ü Dinkelbach; Fred H Hamker
Journal:  Front Neuroinform       Date:  2015-07-31       Impact factor: 4.081

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