Equation-oriented specification of neural models for simulations

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Title: Equation-oriented specification of neural models for simulations
Author(s): Stimberg, M
Goodman, DF
Benichoux, V
Brette, R
Item Type: Journal Article
Abstract: Simulating biological neuronal networks is a core method of research in computational neuroscience. A full specification of such a network model includes a description of the dynamics and state changes of neurons and synapses, as well as the synaptic connectivity patterns and the initial values of all parameters. A standard approach in neuronal modeling software is to build network models based on a library of pre-defined components and mechanisms; if a model component does not yet exist, it has to be defined in a special-purpose or general low-level language and potentially be compiled and linked with the simulator. Here we propose an alternative approach that allows flexible definition of models by writing textual descriptions based on mathematical notation. We demonstrate that this approach allows the definition of a wide range of models with minimal syntax. Furthermore, such explicit model descriptions allow the generation of executable code for various target languages and devices, since the description is not tied to an implementation. Finally, this approach also has advantages for readability and reproducibility, because the model description is fully explicit, and because it can be automatically parsed and transformed into formatted descriptions. The presented approach has been implemented in the Brian2 simulator.
Publication Date: 4-Feb-2014
Date of Acceptance: 14-Jan-2014
ISSN: 1662-5196
Publisher: Frontiers Media
Journal / Book Title: Frontiers in Neuroinformatics
Volume: 8
Copyright Statement: © 2014 Stimberg, Goodman, Benichoux and Brette. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Keywords: computational neuroscience
Publication Status: Published
Article Number: 6
Appears in Collections:Faculty of Engineering
Electrical and Electronic Engineering

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