Imperial College London

Dr Dan Goodman

Faculty of EngineeringDepartment of Electrical and Electronic Engineering

Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 6264d.goodman Website

 
 
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Location

 

1001Electrical EngineeringSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Stimberg:2014:10.3389/fninf.2014.00006,
author = {Stimberg, M and Goodman, DFM and Benichoux, V and Brette, R},
doi = {10.3389/fninf.2014.00006},
journal = {Front Neuroinform},
title = {Equation-oriented specification of neural models for simulations.},
url = {http://dx.doi.org/10.3389/fninf.2014.00006},
volume = {8},
year = {2014}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - 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.
AU - Stimberg,M
AU - Goodman,DFM
AU - Benichoux,V
AU - Brette,R
DO - 10.3389/fninf.2014.00006
PY - 2014///
SN - 1662-5196
TI - Equation-oriented specification of neural models for simulations.
T2 - Front Neuroinform
UR - http://dx.doi.org/10.3389/fninf.2014.00006
UR - https://www.ncbi.nlm.nih.gov/pubmed/24550820
UR - http://hdl.handle.net/10044/1/40621
VL - 8
ER -