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bioRxiv · 10.1101/2020.12.15.422958

Python Inferfaces for the Smoldyn Simulator

Andrews, S. S.·Singh, D.
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Abstract

MotivationSmoldyn 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. ResultsWe 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. AvailabilitySmoldyn 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. Contactsteven.s.andrews@gmail.com Supplementary informationDocumentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html.

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Andrews, S. S., Singh, D.. 2020-12-16. Python Inferfaces for the Smoldyn Simulator. https://doi.org/10.1101/2020.12.15.422958

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