Pycellerator: an arrow-based reaction-like modelling language for biological simulations. Results: Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica. Availability and implementation: All software is available (GPL) from the github repository at Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information.

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  1. Mjolsness, Eric: Prospects for declarative mathematical modeling of complex biological systems (2019)