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GECKO 3.0.0
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@edkerk edkerk released this 05 Mar 23:51
· 148 commits to main since this release
v3.0.0
d113678

After significant refactoring of the codebase, GECKO 3 is more user-friendly, flexibile and versatile than before.

Most notable changes:

  • ecModels have an .ec structure containing all enzyme and kcat information.
  • Enzymes are incorporated in the S-matrix as MW/kcat (previously this was 1/kcat, where the MW was instead considered in the protein exchange reactions).
  • ecModels can be stored in YAML file format that retains all model content.
  • The model-provided list of EC numbers can be used.
  • Various kcat sources can easily be combined.
  • DLKcat is distributed as part of GECKO, as alternative kcat source.
  • Enzyme complex data can be gathered and considered.
  • All model-specific files and scripts are kept in the userData subfolder.
  • Model-specific modelAdapter files contain parameters that are used in model reconstruction and analysis.
  • Because of the above, there is virtually no backwards compatibility with GECKO versions 1 and 2, regarding both models and code.
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