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Software Designed to Model, Visualize Brain Circuits

NetPyNE GUI screen

Detailed models of cortical neurons simulated and visualized in the NetPyNE GUI. (MetaCell)

20 Oct. 2020. An academic-industry team designed a web-based software tool to ease the computer modeling, simulation, and visualization of the brain’s nerve cell circuits. The NetPyNE graphical user interface, or GUI, is a product of the State University of New York Downstate Health Sciences University in Brooklyn, New York and neuroscience software company MetaCell in Cambridge, Massachusetts.

NetPyNE — short for Networks using Python and NEURON — is software for neuro- and data scientists to run research data and simulate the effects on neurons, or nerve cells, in the brain. The software combines the capabilities of NEURON, a simulation language for modeling individual neurons or networks, with the web programming language Python. With NetPyNE, neuroscientists can test assumptions and simulate effects using the NEURON package, by programming instructions with Python, a high-level general-purpose programming language for the web.

Developers of NetPyNE, led by Salvador Durá-Bernal, professor of physiology and pharmacology at SUNY Downstate, describe the software in an article appearing last year in the journal eLife. The team outlines NetPyNE’s capabilities to capture, model, and visualize data at the levels of individual molecules, cells, and circuits. NetPyNE also enables neuroscientists to provide specifications and parameters, and build sophisticated brain models without writing computer code, including an early GUI version.

More recently, Durá-Bernal’s lab and MetaCell upgraded the NetPyNE GUI to expand the tasks it can perform and make it easier to use for neuroscientists. The GUI updates, say the developers, allow users to define network models, run simulations, and visualize cells and networks in three dimensions. The latest version also offers a synchronized control panel that enables users to toggle between Python code and visual mode.

MetaCell says the GUI is now integrated with two online neuroscience resources: Open Source Brain and the Human Brain Project E-BRAINS. And, as with the original NetPyNE, data models can be exported in standard NeuroML and Sonata formats.

“One of our ultimate goals,” says Durá-Bernal in a MetaCell statement, “is to make this tool user-friendly enough such that the ‘non-computational community’ can use it to, for example, predict outcomes of specific neuromodulatory techniques, or model circuit deficits underlying specific neuropsychiatric disorders like schizophrenia.”

Matteo Cantarelli, co-founder of MetaCell and now the company’s chief technology officer adds, “Researchers who take advantage of the new NetPyNE GUI will be able to run thousands of parallel simulations to explore how a range of parameters impact neuronal circuits.”

An online version of the NetPyNE GUI is available at at And NetPyNE GUI documentation is available on GitHub.

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