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++ applicaton 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 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.
Contact steven.s.andrews{at}gmail.com
Supplementary information Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.
Competing Interest Statement
The authors have declared no competing interest.