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

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

FindSim - A Framework for Integrating Neuronal Data and Signaling Models

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

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

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

COBRApy 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

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

BioNetGen 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.

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".