Neurosim Lab   @  Downstate/KCHC

Software

Our lab has been dedicated to the dissemination of open-source software since 1992. Almost all of this software is for use with the NEURON simulation system. Most of the software is from specific models, both from our papers and from those of others posted on ModelDB. We also offer some analysis tools hosted on SimToolDB and simulation management tools on this website.

This page is divided into the following categories:

In addition, there are simulations and exercises available for use with the textbook From Computer to Brain.

Our latest tool is NetPyNE: a Python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.



Models from our papers

Virtually all of our modeling papers are distributed along with source code via ModelDB.



Simulation and analysis tools

The following are simulation or analysis tools. Analysis tools may be utilized for physiological or simulation data. Note that the posted versions of these tools are not always kept current; contact us for current versions if you want to use them.



Small NEURON scripts

These are mostly minor helper functions for NEURON. Note that some of these tools are now deprecated since similar or identical tools can now be accessed via NEURON's PYTHON interface.



Ported models

We depend on the kindness of strangers in developing our simulations and post models of others that we have successfully ported to NEURON (yes, there were a few that were not entirely successful -- i.e. couldn't quite replicate the figures)