Biochemical Networks Python Packages

biosimulators-test-suite

Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators

biomass

A Python Framework for Modeling and Analysis of Signaling Systems

biosimulators-copasi

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

metevolsim

MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.

biosimulators-tellurium

tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

biosimulators-gillespy2

GillesPy2 biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

biosimulators-cobrapy

COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

biosimulators-bionetgen

BioNetGen biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

pasmopy

Patient-Specific Modeling in Python

life123

Dynamical modeling of biological systems in 1, 2 and 3D - incl. diffusion, reactions & compartments. A platform for quantitative reactomics (Python, JupyterLab, Plotly)