The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

A Python framework for structural systems biology

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

Safe Pontryagin Differentiable Programming (Safe PDP) is a new theoretical and algorithmic safe differentiable framework to solve a broad class of safety-critical learning and control tasks.

A Python Library for modeling combinatorial constrained problems

High-level, high-performance, constraint-based reconstruction and analysis in Julia

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Constraint-Based Reconstruction and EXascale Analysis

EMBL GEMs: A collection of GEnome-scale Models for bacterial species

Visualization of metabolic models in Makie.

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.

Repository of tutorials for The COBRA Toolbox

CBMPy is a Python based platform for constraint based modelling and analysis.

Genome-scale metabolic model of Methylococcus capsulatus.

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

Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam

Constraint-based modeling of metabolism using Mixed Integer Optimization

COnstraint Based Reconstruction and EXascale Analysis (in Julia)

Genome-scale model of Yarrowia lipolytica.

Models (and data) of constrained problems developped with the library PyCSP3