Dura-Bernal, S;
Suter, BA;
Gleeson, P;
Cantarelli, M;
Quintana, A;
Rodriguez, F;
Kedziora, DJ;
... Lytton, WW; + view all
(2019)
NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
eLife
, 8
, Article e44494. 10.7554/eLife.44494.
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Abstract
Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, e.g. connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis - connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.
| Type: | Article |
|---|---|
| Title: | NetPyNE, a tool for data-driven multiscale modeling of brain circuits |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.7554/eLife.44494 |
| Publisher version: | https://doi.org/10.7554/eLife.44494 |
| Language: | English |
| Additional information: | © Copyright Dura-Bernal et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. |
| Keywords: | Computational biology, neuroscience, systems biology |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Neuro, Physiology and Pharmacology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10073411 |
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