Literature DB >> 17873374

Interoperability of neuroscience modeling software: current status and future directions.

Robert C Cannon1, Marc-Oliver Gewaltig, Padraig Gleeson, Upinder S Bhalla, Hugo Cornelis, Michael L Hines, Fredrick W Howell, Eilif Muller, Joel R Stiles, Stefan Wils, Erik De Schutter.   

Abstract

Neuroscience increasingly uses computational models to assist in the exploration and interpretation of complex phenomena. As a result, considerable effort is invested in the development of software tools and technologies for numerical simulations and for the creation and publication of models. The diversity of related tools leads to the duplication of effort and hinders model reuse. Development practices and technologies that support interoperability between software systems therefore play an important role in making the modeling process more efficient and in ensuring that published models can be reliably and easily reused. Various forms of interoperability are possible including the development of portable model description standards, the adoption of common simulation languages or the use of standardized middleware. Each of these approaches finds applications within the broad range of current modeling activity. However more effort is required in many areas to enable new scientific questions to be addressed. Here we present the conclusions of the "Neuro-IT Interoperability of Simulators" workshop, held at the 11th computational neuroscience meeting in Edinburgh ( July 19-20 2006; http://www.cnsorg.org ). We assess the current state of interoperability of neural simulation software and explore the future directions that will enable the field to advance.

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Year:  2007        PMID: 17873374      PMCID: PMC2658651          DOI: 10.1007/s12021-007-0004-5

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


  19 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.  Opinion: Sharing primary data: a threat or asset to discovery?

Authors:  Stephen H Koslow
Journal:  Nat Rev Neurosci       Date:  2002-04       Impact factor: 34.870

3.  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

4.  Towards effective and rewarding data sharing.

Authors:  Daniel Gardner; Arthur W Toga; Giorgio A Ascoli; Jackson T Beatty; James F Brinkley; Anders M Dale; Peter T Fox; Esther P Gardner; John S George; Nigel Goddard; Kristen M Harris; Edward H Herskovits; Michael L Hines; Gwen A Jacobs; Russell E Jacobs; Edward G Jones; David N Kennedy; Daniel Y Kimberg; John C Mazziotta; Perry L Miller; Susumu Mori; David C Mountain; Allan L Reiss; Glenn D Rosen; David A Rottenberg; Gordon M Shepherd; Neil R Smalheiser; Kenneth P Smith; Tom Strachan; David C Van Essen; Robert W Williams; Stephen T C Wong
Journal:  Neuroinformatics       Date:  2003

5.  From biophysics to behavior: Catacomb2 and the design of biologically-plausible models for spatial navigation.

Authors:  Robert C Cannon; Michael E Hasselmo; Randal A Koene
Journal:  Neuroinformatics       Date:  2003

6.  ModelDB: making models publicly accessible to support computational neuroscience.

Authors:  Michele Migliore; Thomas M Morse; Andrew P Davison; Luis Marenco; Gordon M Shepherd; Michael L Hines
Journal:  Neuroinformatics       Date:  2003

7.  A sodium channel gating model based on single channel, macroscopic ionic, and gating currents in the squid giant axon.

Authors:  C A Vandenberg; F Bezanilla
Journal:  Biophys J       Date:  1991-12       Impact factor: 4.033

Review 8.  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

9.  Mechanism of gating of T-type calcium channels.

Authors:  C F Chen; P Hess
Journal:  J Gen Physiol       Date:  1990-09       Impact factor: 4.086

10.  Neuroscience networks: data-sharing in an information age.

Authors:  Thomas R Insel; Nora D Volkow; Ting-Kai Li; James F Battey; Story C Landis
Journal:  PLoS Biol       Date:  2003-10-13       Impact factor: 8.029

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  37 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.  KInNeSS: a modular framework for computational neuroscience.

Authors:  Massimiliano Versace; Heather Ames; Jasmin Léveillé; Bret Fortenberry; Anatoli Gorchetchnikov
Journal:  Neuroinformatics       Date:  2008-08-10

3.  STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python.

Authors:  Stefan Wils; Erik De Schutter
Journal:  Front Neuroinform       Date:  2009-06-29       Impact factor: 4.081

4.  The International Neuroinformatics Coordinating Facility: evaluating the first years.

Authors:  Erik De Schutter
Journal:  Neuroinformatics       Date:  2009-07-28

5.  Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models.

Authors:  Tiina Manninen; Katri Hituri; Eeva Toivari; Marja-Leena Linne
Journal:  EURASIP J Bioinform Syst Biol       Date:  2011-03-29

6.  Visualizing neuronal network connectivity with connectivity pattern tables.

Authors:  Eilen Nordlie; Hans Ekkehard Plesser
Journal:  Front Neuroinform       Date:  2010-01-29       Impact factor: 4.081

7.  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

8.  Towards reproducible descriptions of neuronal network models.

Authors:  Eilen Nordlie; Marc-Oliver Gewaltig; Hans Ekkehard Plesser
Journal:  PLoS Comput Biol       Date:  2009-08-07       Impact factor: 4.475

9.  [Not Available].

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

10.  PyMOOSE: Interoperable Scripting in Python for MOOSE.

Authors:  Subhasis Ray; Upinder S Bhalla
Journal:  Front Neuroinform       Date:  2008-12-19       Impact factor: 4.081

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