Vivarium-Bioscrape

Vivarium-bioscrape is a python package connecting the multiscale simulation framework Vivarium to the chemical reaction network (CRN) simulator Bioscrape. In particular, this package wraps bioscrape as a vivarium Process and includes a number of Derivers in the form of OneWayMaps to help connect CRNs to eachother and other processes.

Visit the Vivarium Core documentation to learn how to use the core Vivarium engine to create computational biology models.

Visit the Bioscrape Wiki to learn about the bioscrape simulator and find bioscrape usage examples.

Installation

The easiest way to install this package is via:

pip install vivarium-bioscrape 

(with Python>=3.7)

This command will automatically install the package along with vivarium-core and bioscrape and all othe dependencies.

Please note that Bioscrape is a cython extension module and requires a C++ compiler to be set up on your computer for installation. Please visit the Bioscrape Wiki for more information.

You can then run the vivarium-bioscrape process with the module format:

$ python -m vivarium_bioscrape.processes.bioscrape