The purpose of this document is to solicit community feedback on NetPyNE, which was submitted to INCF for endorsement as a standard. The document contains the INCF Standards and Best Practices Committee's review of NetPyNE, and the criteria in which it was evaluated (open, FAIR, testing and implementation, governance, adoption and use, stability and support, and comparison to similar standards). For the next 60 days, we are seeking community feedback on NetPyNE.
About NetPyNE:
NetPyNE is an open-source Python package designed for the development, simulation, and analysis of biological neuronal networks. Built on top of the widely used NEURON simulator, NetPyNE is a high-level interface for creating, managing, and simulating complex neural network models using declarative network specification. Integrating all the major steps of the modeling workflow under a single framework, NetPyNE enables users to define their model across scales, from molecules to neurons to circuits. Included are tools for analyzing and visualizing simulation results, which have been used in the rendering of various detailed models of the motor, auditory, and somatosensory thalamocortical circuits, and of spinal cord circuits in various peer-reviewed publications. Users can get started by consulting the comprehensive documentation, tutorials, and examples which have already been generated by the growing NetPyNE community.
Summary of Discussion:
NetPyNE conforms to the main criteria outlined by INCF for consideration for endorsement. It is open-source and designed around the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. NetPyNE is well documented with good test coverage and is governed by a volunteer steering committee led by documented goals and standards. There are multiple forums in which NetPyNE users and developers interact. A number of tutorials are available including interactive Jupyter notebooks and YouTube videos. There is a large and growing user community with dozens of ongoing projects utilizing NetPyNE. NetPyNE is currently supported by a five-year grant from the National Institutes of Health (NIH), and we will apply to extend that grant. While there are other INCF SBPs that cover portions of the capabilities, NetPyNE is unique in multiple modeling scales (from molecules to brains) and its breadth of function (import/export, network specification, parallel simulation, variety of analyses, and optimization of parameters).
Recommendation:
The INCF Standards and Best Practices Committee voted to put the NetPyNE format forward for Community Review.
No competing interests were disclosed
Comments
Tue, 01/02/2024 - 19:41
Thu, 01/18/2024 - 19:30
Tue, 01/23/2024 - 03:22
Fri, 02/09/2024 - 15:43
Its easy-to-use descriptive syntax and the online GUI are great for getting beginners started.
The tool also offers support to the most recent features of the NEURON simulator, such as the Reaction-Diffusion toolbox, to model interactions at the molecular level.
It also supports standardized data-sharing formats, such as the SONATA guidelines.
Overall, NetPyNE is a great tool and has been fundamental in the development of my PhD work.
I'm part of Dr. Dura-Bernal's lab, the developer of NetPyNE.