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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 folder, protocol.m contains instructions on how to reconstruct and analyze an ecModel for S. cerevisiae. This demonstrates how many of GECKO's functions can be used.

💡 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. The source code documentation is also available online.

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

Citation

• A GECKO 3 publication is currently under consideration, citation information will appear here in due course.
• For GECKO release 2, please cite Domenzain et al. (2022) doi:10.1038/s41467-022-31421-1.
• For GECKO release 1, please cite Sánchez et al. (2017) doi:10.15252/msb.20167411.