@article{146dcbaf7364425499736b5b1f103101,
title = "NetpyNE, a tool for data-driven multiscale modeling of brain circuits",
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, for example 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.",
author = "Salvador Dura-Bernal and Suter, {Benjamin A.} and Padraig Gleeson and Matteo Cantarelli and Adrian Quintana and Facundo Rodriguez and Kedziora, {David J.} and Chadderdon, {George L.} and Kerr, {Cliff C.} and Neymotin, {Samuel A.} and McDougal, {Robert A.} and Michael Hines and Shepherd, {Gordon M.G.} and Lytton, {William W.}",
note = "Funding Information: This work was funded by grants from the NIH, NSF, NYS SCIRB, UK Welcome Trust and Australian Research Council, which are listed in detail below. We are thankful to all the contributors that have collaborated in the development of this open source tool via GitHub (https://github.com/Neurosim-lab/netpyne). Funding Information: NIBIBNational Institute of Biomedical Imaging and BioengineeringU01EB017695 Salvador Dura-Bernal Benjamin A Suter Matteo Cantarelli Adrian Quintana Facundo Rodriguez Samuel A Neymotin Michael Hines Gordon MG Shepherd William W Lytton New York State Department of Health DOH01-C32250GG-3450000 Salvador Dura-Bernal Facundo Rodriguez William W Lytton Wellcome Trust 101445 Padraig Gleeson National Institute on Deafness and Other Communication Disorders R01DC012947-06A1 Samuel A Neymotin National Institute of Biomedi- cal Imaging and Bioengineer- ing R01EB022903 Salvador Dura-Bernal Michael Hines William W Lytton National Institute of Mental Health R01MH086638 Robert A McDougal Michael Hines William W Lytton Wellcome Trust 212941 Padraig Gleeson National Institute of Biomedical Imaging and Bioengineering R01EB022889 Salvador Dura-Bernal Matteo Cantarelli Adrian Quintana Facundo Rodriguez Samuel A Neymotin Michael Hines ARC Australian Research Council DE140101375 David J Kedziora Cliff C Kerr The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.",
year = "2019",
month = apr,
doi = "10.7554/eLife.44494",
language = "English (US)",
volume = "8",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
}