Overview: NetPyNE is an NIH-funded tool for data-driven multiscale modeling of brain circuits. It enables users to consolidate complex experimental data from different brain scales into a unified mechanistic computational model. NetPyNE builds on top of NEURON, one of the most widely used neural simulation engines. NetPyNE is unique integrating all major steps of the modeling workflow under a single framework. The core of NetPyNE consists of a standardized JSON-like declarative language that allows the user to define the model across scales, from molecules to neurons to circuits. The NetPyNE API can then be used to automatically generate the corresponding NEURON network, run parallel simulations, optimize and explore parameters, and visualize and analyze the results through a wide range of built-in functions.
Graphical Web Application: All functionality is also available via a state-of-the art web-based graphical application, which now includes management of simulations and automated exploration of parameters. This is the only graphical tool that allows users to define parameters values to explore, run the corresponding simulations and visualize the results. Additionally, the web app is fully integrated with the Open Source Brain (OSB) platform, providing users with an online persistent workspace, file management, access to online resources and interactive jupyter notebooks.
Interface/integration with other tools and standards: NetPyNE facilitates model sharing by exporting/importing to the NeuroML and SONATA standardized formats. It has been interfaced with CoreNEURON, and several large-scale models were benchmarked on GPUs for the first time, obtaining impressive 40x speedups. The interface with the LFPykit tool allows NetPyNE to generate dipole current moments for any arbitrary model, and simulate EEG signals at electrodes placed along a head volume conduction model. Similiar EEG/MEG measures can also be obtained through an interface with the Human Neocortical Neurosolver (HNN) tool. The new co-simulation interface between NetPyNE and The Virtual Brain (TVB) achieves a new milestone for multiscale modeling: linking molecular chemical signaling (via RxD) to whole-brain network dynamics. NetPyNE is now also available as an official service on the Human Brain Project EBRAINS platform (https://www.ebrains.eu/tools/netpyne). The SciUnit tool has been adapted to work with NetPyNE, resulting in the NetPyNEUnit package which facilitates model reproducibility, validation and evaluation.
User community: At least 25 publications describe models or tools that have made use of NetPyNE, including our recent detailed models of the motor, auditory and somatosensory thalamocortical circuits, and of spinal cord circuits. Others have developed NetPyNE models to study Parkinson's disease, schizophrenia, ischemic stroke and epilepsy.
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Grant Funding:
Research Grants making use of NetPyNE:
Current Core Developers:
Previous Core Developers:
Major Contributors:
Governance Structure:
Major decisions about NetPyNE are made by the steering committee, guided by the Project roadmap and the Code of conduct. The committee includes members from a diverse range of institutions, positions and backgrounds. The current steering committee consists of the following members (in alphabetical order):
Questions, Suggestions, Contributions
Two kinds of contributions are solicited: 1. direct contributions to NetPyNE code described below. 2. Ancillary code contributions.
NetPyNE is open-source and available at https://github.com/suny-downstate-medical-center
For questions or suggestions please use the NetPyNE forum, the NEURON+NetPyNE forum or submit an issue to GitHub.
Contributions are gladly welcome! Please fork the repository and make a Pull Request with your changes. See our Contributors Guide for more details.
Code of Conduct
This project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
Please read the full Code of Conduct.
The current project roadmap encompasses four major categories: quality control, GUI extension, dissemination and community engagement, and development of new features. This roadmap was initially established under a primary 5-year NIH grant and has since been extended due to additional funding and continued progress. Below are the main objectives and estimated timelines:
Extension of the graphical user interface (GUI), essential to engage new users and make the tool accessible to experimentalists, clinicians and students.
We will implement complementary dissemination and engagement strategies to train and attract users and developers:
