GECKO Toolbox

Version 3.2.1 (26.2 MB) by Eduard Kerkhoven
Toolbox for including enzyme constraints in a genome-scale model.
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Updated 7 Jun 2024
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About GECKO 3.0

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.

💡 In the GECKO/tutorials folder there are examples of how GECKO can be applied to GEMs, in either of its full or light forms. Each protocol.m contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. These two scripts complement the protocols paper.

Significant changes since protocol publication

  • GECKO 3.2.0: all protein usage reactions draw from the protein pool, even if they are constrained by proteomics data. This affects Step 58 in the protocol, changing behaviour of constrainEnzConcs and making updateProtPool obsolete, tutorials/full_ecModel/protocol.m is updated to reflect this change. See #357 for more details.

Note: Regarding code and model compatibility with earlier GECKO versions, see Previous versions: GECKO 1 and 2.

Cite us

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. 2024 Jan 18:1-39. doi: 10.1038/s41596-023-00931-7

Documentation

Installation instructions and other information is available in the Wiki. The source code documentation is also available online. Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the contributing guidelines to get started.

Cite As

Eduard Kerkhoven (2024). GECKO Toolbox (https://github.com/SysBioChalmers/GECKO/releases/tag/v3.2.1), GitHub. Retrieved .

Chen, Yu, et al. “Reconstruction, Simulation and Analysis of Enzyme-Constrained Metabolic Models Using GECKO Toolbox 3.0.” Nature Protocols, vol. 19, no. 3, Springer Science and Business Media LLC, Jan. 2024, pp. 629–67, doi:10.1038/s41596-023-00931-7.

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MATLAB Release Compatibility
Created with R2022a
Compatible with R2019b and later releases
Platform Compatibility
Windows macOS Linux
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src/geckomat/change_model

src/geckomat/gather_kcats

src/geckomat/get_enzyme_data

src/geckomat/kcat_sensitivity_analysis

src/geckomat/kcat_sensitivity_analysis/Bayesian

src/geckomat/limit_proteins

src/geckomat/model_adapter

src/geckomat/utilities

test/manual_tests

test/unit_tests

test/unit_tests/ecTestGEM

tutorials/full_ecModel

tutorials/full_ecModel/code

tutorials/light_ecModel

tutorials/light_ecModel/code

Version Published Release Notes
3.2.1

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.2.1
3.2.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.2.0
3.1.3

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.1.3
3.1.2.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.1.2
3.1.1.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.1.1
3.1.0.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.1.0
3.0.2.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.0.2
3.0.1

3.0.0.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v3.0.0
2.0.3.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v2.0.3
2.0.2.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v2.0.2
2.0.1.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v2.0.1
2.0.0.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v2.0.0
1.3.5.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.3.5
1.3.4.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.3.4
1.3.3.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.3.3
1.3.2.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.3.2
1.3.1.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.3.1
1.3.0.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.3.0
1.2.1.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.2.1
1.2.0.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.2.0
1.1.2.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.1.2
1.1.1.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.1.1
1.1.0.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.1.0
1.0.0.0

See release notes for this release on GitHub: https://github.com/SysBioChalmers/GECKO/releases/tag/v1.0
To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.