COBRApy is a package for constraint-based modeling of metabolic networks.

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

Spatial bio-chemical reaction model editor and simulator

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

Interface between the Systems Biology Markup Language and Julia

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.

sbml2hyb is a tool for SBML compatible hybrid modelling of biological systems

Easily use the memote command line interface from a docker container.

Python package and workflow for EFM calculation via (mp)lrs and efmtool

Python package for managing systems and subsystems of SBML models

A graphical editor for systems biology models.

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

Python utilities for SBML extended for cpp

Test and grade genome-scale metabolic models (GEMs).

Hepatocyte model of ischemia reperfusion injury (IRI)

Final Infobiotics Workbench implementation of SBOL and SBML conversion functionality, UI updates, and sequence fetching