The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

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

Computational synthetic biology: Predicting DNA edits for bioengineering

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!

Reinforcement Learning based bioretrosynthesis tool

Infer metabolic directions from moment differences of mass-weighted intensity distributions

teemi: A Python package for reproducible and FAIR microbial strain construction. Simulate the entire dbtl-cycle, generate genetic parts, design libraries, and track samples. Open-source Python platform for workflow flexibility and automated tasks, accelerating metabolic engineering. Try teemi with our Google Colab notebooks!

Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL

COnstraint Based Reconstruction and EXascale Analysis (in Julia)

A Universal Modeling Language for Metabolic Flux Analysis

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Genome-scale model of Yarrowia lipolytica.

Python wrapper for Retropath2.0 Knime workflow

Suite of tools that work on rpSBML format

Diversity-based enumeration of optimal context-specific metabolic networks

Library to perform metabolic engineering tasks

Enzymatic Link Prediction

Context-sensitive creation of kinetic equations in biochemical networks

Determination of product-growth-coupled strain designs employing stoichiometric metabolic models.