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
Dynamical modeling of biological systems in 1, 2 and 3D - incl. diffusion, reactions & compartments. A platform for quantitative reactomics (Python, JupyterLab, Plotly)
Context-sensitive creation of kinetic equations in biochemical networks
MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
Web-Based Biochemical Kinetics Editor 🧪✨
COPASI 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
Hybrid kinetic models for small biochemical networks: learn the unknown rate laws from time-series data, then recover them symbolically
COBRApy 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
Preserved mathematical and computational biology work with reproducible code and evidence. Research stopped at the owner's request on 2026-10-31.
A generalized biochemical simulation framework
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
Tropical Sensitivity Scores
Julia interface to BioMASS
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