Literature DB >> 22994683

Creating, documenting and sharing network models.

Sharon M Crook1, James A Bednar, Sandra Berger, Robert Cannon, Andrew P Davison, Mikael Djurfeldt, Jochen Eppler, Birgit Kriener, Steve Furber, Bruce Graham, Hans E Plesser, Lars Schwabe, Leslie Smith, Volker Steuber, Sacha van Albada.   

Abstract

As computational neuroscience matures, many simulation environments are available that are useful for neuronal network modeling. However, methods for successfully documenting models for publication and for exchanging models and model components among these projects are still under development. Here we briefly review existing software and applications for network model creation, documentation and exchange. Then we discuss a few of the larger issues facing the field of computational neuroscience regarding network modeling and suggest solutions to some of these problems, concentrating in particular on standardized network model terminology, notation, and descriptions and explicit documentation of model scaling. We hope this will enable and encourage computational neuroscientists to share their models more systematically in the future.

Mesh:

Year:  2012        PMID: 22994683     DOI: 10.3109/0954898X.2012.722743

Source DB:  PubMed          Journal:  Network        ISSN: 0954-898X            Impact factor:   1.273


  10 in total

1.  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

Review 2.  Connectivity concepts in neuronal network modeling.

Authors:  Johanna Senk; Birgit Kriener; Mikael Djurfeldt; Nicole Voges; Han-Jia Jiang; Lisa Schüttler; Gabriele Gramelsberger; Markus Diesmann; Hans E Plesser; Sacha J van Albada
Journal:  PLoS Comput Biol       Date:  2022-09-08       Impact factor: 4.779

3.  Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations.

Authors:  Sacha Jennifer van Albada; Moritz Helias; Markus Diesmann
Journal:  PLoS Comput Biol       Date:  2015-09-01       Impact factor: 4.475

4.  Efficient generation of connectivity in neuronal networks from simulator-independent descriptions.

Authors:  Mikael Djurfeldt; Andrew P Davison; Jochen M Eppler
Journal:  Front Neuroinform       Date:  2014-04-22       Impact factor: 4.081

5.  Handling Metadata in a Neurophysiology Laboratory.

Authors:  Lyuba Zehl; Florent Jaillet; Adrian Stoewer; Jan Grewe; Andrey Sobolev; Thomas Wachtler; Thomas G Brochier; Alexa Riehle; Michael Denker; Sonja Grün
Journal:  Front Neuroinform       Date:  2016-07-19       Impact factor: 4.081

6.  Constructing Neuronal Network Models in Massively Parallel Environments.

Authors:  Tammo Ippen; Jochen M Eppler; Hans E Plesser; Markus Diesmann
Journal:  Front Neuroinform       Date:  2017-05-16       Impact factor: 4.081

7.  Performance Comparison of the Digital Neuromorphic Hardware SpiNNaker and the Neural Network Simulation Software NEST for a Full-Scale Cortical Microcircuit Model.

Authors:  Sacha J van Albada; Andrew G Rowley; Johanna Senk; Michael Hopkins; Maximilian Schmidt; Alan B Stokes; David R Lester; Markus Diesmann; Steve B Furber
Journal:  Front Neurosci       Date:  2018-05-23       Impact factor: 4.677

8.  Equation-oriented specification of neural models for simulations.

Authors:  Marcel Stimberg; Dan F M Goodman; Victor Benichoux; Romain Brette
Journal:  Front Neuroinform       Date:  2014-02-04       Impact factor: 4.081

9.  morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python.

Authors:  Michael J Hull; David J Willshaw
Journal:  Front Neuroinform       Date:  2014-01-28       Impact factor: 4.081

Review 10.  Modeling the Cerebellar Microcircuit: New Strategies for a Long-Standing Issue.

Authors:  Egidio D'Angelo; Alberto Antonietti; Stefano Casali; Claudia Casellato; Jesus A Garrido; Niceto Rafael Luque; Lisa Mapelli; Stefano Masoli; Alessandra Pedrocchi; Francesca Prestori; Martina Francesca Rizza; Eduardo Ros
Journal:  Front Cell Neurosci       Date:  2016-07-08       Impact factor: 5.505

  10 in total

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