A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

A Python Framework for Modeling and Analysis of Signaling Systems

Patient-Specific Modeling in Python

FindSim - A Framework for Integrating Neuronal Data and Signaling Models

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

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

Context-sensitive creation of kinetic equations in biochemical networks

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

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

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

R package associated with paper "Component response rate variation underlies the stability of highly complex finite systems" (Duthie, AB. 2020. Sci. Rep. 10:8296, https://www.nature.com/articles/s41598-020-64401-w). This repository contains all manuscript text and supplemental information, and all code for recreating analyses.

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

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

Another Genetic Circuit Transcriber

Julia interface to BioMASS

Tropical Sensitivity Scores

This repository is used to determine the settling time of a given biochemical reaction network using the approach described in the manuscript "An Automated Model Reduction Method for Biochemical Reaction Networks" published in "Symmetry".