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Installation instructions

About GECKO 3

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. The source code documentation is also available online.

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.

Citation

To refer to GECKO in general, or if you have used GECKO release 3 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.

To specifically cite GECKO release 2: Domenzain et al. (2022) doi:10.1038/s41467-022-31421-1.

To specifically cite GECKO release 1: Sánchez et al. (2017) doi:10.15252/msb.20167411.