Abstract
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. 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. 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.
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