constraint-based-modeling
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The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
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Dec 10, 2025 - MATLAB
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
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Dec 11, 2025 - MATLAB
A Python framework for structural systems biology
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Dec 7, 2020 - Python
A Python Library for modeling combinatorial constrained problems
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Dec 17, 2025 - Python
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.
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Jul 23, 2022 - Python
High-level, high-performance, constraint-based reconstruction and analysis in Julia
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Apr 26, 2023 - 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!
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Dec 18, 2025 - Python
Constraint-Based Reconstruction and EXascale Analysis
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Oct 23, 2024 - Julia
EMBL GEMs: A collection of GEnome-scale Models for bacterial species
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Mar 5, 2019
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.
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Oct 24, 2025 - HTML
Repository of tutorials for The COBRA Toolbox
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Dec 5, 2025 - MATLAB
Visualization of metabolic models in Makie.
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Feb 15, 2025 - Julia
CBMPy is a Python based platform for constraint based modelling and analysis.
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May 12, 2024 - Python
COnstraint Based Reconstruction and EXascale Analysis (in Julia)
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Sep 26, 2025 - Julia
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
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Mar 20, 2024 - Jupyter Notebook
Python, modeling and Flux balance analysis tutorials for the undergraduate Systems Biology course in Amsterdam
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Jun 30, 2019 - Jupyter Notebook
Constraint-based modeling of metabolism using Mixed Integer Optimization
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Sep 24, 2024 - Python
Genome-scale metabolic model of Methylococcus capsulatus.
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Apr 12, 2019 - HTML
Models (and data) of constrained problems developped with the library PyCSP3
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Dec 15, 2025 - Python
Genome-scale model of Yarrowia lipolytica.
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Jul 30, 2021 - MATLAB
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