amici
High-performance sensitivity analysis for large ordinary differential equation models
parpe
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
cobra
COBRApy is a package for constraint-based modeling of metabolic networks.
SBMLToolkit
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
sbml2julia
A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.
https://github.com/biosimulators/biosimulators_copasi
COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
https://github.com/biosimulators/biosimulators_test_suite
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
findcpcli
findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
https://github.com/cthoyt/biomodels-metadata-analysis
Generate a summary of metadata annotations in the BioModels database
https://github.com/biosimulators/biosimulators_tellurium
tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
https://github.com/biosimulators/biosimulators_pysces
PySCeS biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
https://github.com/biosimulators/biosimulators_amici
AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
https://github.com/biosimulations/biosimulations-bigg
Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations
https://github.com/biosimulators/biosimulators_masspy
MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
https://github.com/charlesrocabert/metevolsim
MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
https://github.com/biosimulators/biosimulators_cobrapy
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
moccasin
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
petab
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
https://github.com/biosimulators/biosimulators
Registry of containerized biosimulation tools that support a standard command-line interface
biosimulations
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
euromix-to-sbml
Antimony/SBML re-implementation of the EuroMix Generic PBK model.
sbmlpkgspec
A LaTeX document class providing a standard format for SBML Level 3 package specification documents.
https://github.com/copasi/copasi-dependencies
Collection of OpenSource libraries to simplify COPASI build
