Previous versions: GECKO 1 and 2

Backwards compatibility with GECKO 3

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 .ec structure 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 gecko2 branch remains available for any potential fixes.

Citation

• 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.