Previous versions: GECKO 1 and 2
Eduard Kerkhoven edited this page Nov 30, 2023
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1 revision
Due to significant refactoring of the code, GECKO version 3 is largely not backwards compatible with earlier GECKO versions.
- Most notably, GECKO 3 ecModels have an
.ecstructure containing all enzyme and kcat information. - In addition, in GECKO 3 enzymes are incorporated in the S-matrix as MW/kcat, while in GECKO 1 and 2 this was 1/kcat (where the MW was instead considered in the protein exchange reactions).
- GECKO 3 ecModels can be stored in YAML file format that retains all model content.
- Most functions in GECKO 3 do not work on ecModels generated with GECKO versions 1 or 2.
- ecModels generated in GECKO 3 do not work with functions from GECKO versions 1 or 2.
- At this moment, there are no Python functions to work with GECKO 3 formatted ecModels.
- The last GECKO 2 release (2.0.3) is available here.
- The
gecko2branch remains available for any potential fixes.
- GECKO release 2: Domenzain et al. (2022) doi:10.1038/s41467-022-31421-1.
- GECKO release 1: Sánchez et al. (2017) doi:10.15252/msb.20167411.