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The GECKO toolbox enhances a Genome-scale model to account for Enzyme Constraints, using Kinetics and Omics. The resulting enzyme-constrained model (ecModel) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data.
GECKO is written in MATLAB. Its Python port, geckopy, reads and writes the same ecModel YAML files, and the two toolboxes are kept in step by a parity ledger. The documentation covers both.
This is GECKO 4.0.0b1. For the changes from GECKO 3, see GECKO 3 → GECKO 4; for the differences between GECKO and geckopy, see GECKO vs. geckopy.
- Install GECKO as described in the installation instructions.
- Follow Getting started and Building an ecModel in the guide, or open
tutorials/full_ecModel/protocol.mortutorials/light_ecModel/protocol.min MATLAB. Each script reconstructs and analyses an ecModel step by step, in its full or light form (GECKO light), and complements the Nature Protocols paper.
The installation instructions, the protocol and the API reference for MATLAB and Python are at gecko-docs. Use GitHub Discussions for questions and comments.
If you have used GECKO in your work, please cite:
Chen Y, Gustafsson J, Tafur Rangel A, Anton M, Domenzain I, Kittikunapong C, Li F, Yuan L, Nielsen J & Kerkhoven EJ. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0. Nature Protocols 19, 629-667 (2024). doi:10.1038/s41596-023-00931-7.
Contributions are welcome. Read the contributing guidelines first. A change to a function that geckopy also has needs the matching change there; the parity ledger lists the pairs.