Python interfaces for the Smoldyn simulator

Abstract

Motivation: Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ application programming interface (API), which were convenient, but limited extensibility.

Results: We added a Python API to Smoldyn to improve integration with other software tools, such as Jupyter notebooks, other Python code libraries and other simulators. It includes low-level functions that closely mimic the existing C/C++ API and higher-level functions that are more convenient to use. These latter functions follow modern object-oriented Python conventions.

Availability and implementation: Smoldyn is open source and free, available at http://www.smoldyn.org and can be installed with the Python package manager pip. It runs on Mac, Windows and Linux.

Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.