Smoldyn

Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions.

More information about Smoldyn is available at http://www.smoldyn.org. Please visit this website to learn about Smoldyn, download the latest release, etc.

Installing Smoldyn

The Smoldyn Python package can be installed by executing the following command.

python3 -m pip install smoldyn

You can also use the Python package to run models written in txt file.

python -m smoldyn model.txt

Compiled binaries for Mac OS and Windows are also available at http://www.smoldyn.org/download.html.

Executing Smoldyn simulations online

Smoldyn simulations can be executed online through runBioSimulations. This requires Smoldyn simulations to be driven by a SED-ML file and packaged into a COMBINE archive. runBioSimulations provides tools for created SED-ML files and COMBINE archives.

Using Smoldyn with SED-ML and COMBINE archives

Smoldyn provides a BioSimulators-compliant interface for executing Smoldyn simulations through SED-ML and COMBINE archives. More information about using Smoldyn with SED-ML and COMBINE archives is available here.

Documentation about simulation algorithms

Information about the simulation algorithms employed by Smoldyn is available at BioSimulators.

Smoldyn source code

This is the official source code repository for Smoldyn. (Formerly this repository was called Smoldyn-official.) This repository is run by Smoldyn's main author, Steve Andrews. The purpose of this repository is enable developers to collaborate on the code for Smoldyn.

Contributing to Smoldyn

New contributions to the code are welcome. To maximize the impact of contributions to Smoldyn, please contact the main author to discuss potential additions. Steve can be reached at steven.s.andrews@gmail.com.