Compartor is an automatic moment equation generator for stochastic compartment populations: From a set of provided interaction rules, it derives the associated system of ODEs that describes the population statistics. Equations can be exported as Python or Julia code.
Install with pip
pip install compartor
Please that the LPAC-related notebooks use the local copy of compartor in the repository, as the pip package is (temporarily) still on version 1.1.1.
A tutorial for the usage of Compartor is provided as Jupyter notebooks at https://github.com/zechnerlab/Compartor. (You can experiment with the notebooks on Binder first, without installing anything locally.)
Compartor is published in
Pietzsch, T., Duso, L., Zechner, C. (2020) Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations. Bioinformatics, 2021, btab058, (https://doi.org/10.1093/bioinformatics/btab058).
Compartor is based on the theoretical framework introduced by
Duso, L. and Zechner, C. (2020). Stochastic reaction networks in dynamic compartment populations. Proceedings of the National Academy of Sciences, 117(37), 22674–22683 (https://doi.org/10.1073/pnas.2003734117).