*Result*: Python interfaces for the Smoldyn simulator.

Title:
Python interfaces for the Smoldyn simulator.
Authors:
Singh, Dilawar1 (AUTHOR), Andrews, Steven S2 (AUTHOR) steven.s.andrews@gmail.com
Source:
Bioinformatics. 1/1/2022, Vol. 38 Issue 1, p291-293. 3p.
Database:
Academic Search Index

*Further Information*

*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. [ABSTRACT FROM AUTHOR]*