Workshop on Multi-Scale Network Modeling Using NEURON/NetPyNE (2019, May)
~~~ LOCATION ~~~
164 Angell St.
~~~ DATE ~~~
Thursday, May 23, 2019
~~~ TIME ~~~
2:00 PM - 4:30 PM
~~~ SPEAKER ~~~
Salvador Dura-Bernal, Ph.D.,
Research Assistant Professor,
State University of New York, Downstate Medical Center
~~~ AGENDA ~~~
2:00 – 2:45 PM: Introduction to multi-scale modeling using NetPyNE and example applications (Seminar-like)
2:45 – 4:30 PM: Hands-on tutorial covering tool installation, building a simple and a complex network, running simulations, visualizing and analyzing network and simulations results, and using the GUI.
~~~ DESCRIPTION ~~~
Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (
) 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, eg. 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 in over 20 labs to teach computational neuroscience students and by modelers to investigate brain regions and phenomena, including cortical circuits, hippocampus, cerebellum, schizophrenia, epilepsy and neurostimulation. It is also being integrated with the Human Neocortical Neurosolver tool (
) developed at Brown.
Field of Study
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