NetPyNE: a tool for data-driven multiscale modeling of brain circuits

Dura-Bernal, S.; Suter, B.; Gleeson, P.; Cantarelli, M.; Quintana, A.; Rodriguez, F.; Kedziora, D. J.; Chadderdon, G. L.; Kerr, C. C.; Neymotin, S. A.; McDougal, R.; Hines, M.; Shepherd, G. M.; Lytton, W. W.

doi:10.1101/461137

bioRxiv · 10.1101/461137

NetPyNE: a tool for data-driven multiscale modeling of brain circuits

Dura-Bernal, S.·Suter, B.·Gleeson, P.·Cantarelli, M.·Quintana, A.·Rodriguez, F.·Kedziora, D. J.·Chadderdon, G. L.·Kerr, C. C.·Neymotin, S. A.·McDougal, R.·Hines, M.·Shepherd, G. M.·Lytton, W. W.

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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., a connectivity rule, instead of tens of loops to create millions of cell-to-cell connections. Users can then 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, raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing using NeuroML and SONATA standardized formats. NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate different brain regions and phenomena.

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Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez, F., Kedziora, D. J., Chadderdon, G. L., Kerr, C. C., Neymotin, S. A., McDougal, R., Hines, M., Shepherd, G. M., Lytton, W. W.. 2018-11-03. NetPyNE: a tool for data-driven multiscale modeling of brain circuits. https://doi.org/10.1101/461137

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