There is a newer version of the record available.

Published March 5, 2023 | Version v3.0.0
Software Open

SysBioChalmers/GECKO: GECKO 3.0.0

Authors/Creators

  • 1. Chr. Hansen
  • 2. Chalmers University of Technology
  • 3. @SysBioChalmers
  • 4. BioInnovation Institute
  • 5. @UnseenBio
  • 6. SINTEF
  • 7. Gitter

Description

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.

Files

SysBioChalmers/GECKO-v3.0.0.zip

Files (22.3 MB)

Name Size Download all
md5:05ef78850fdd9f53dce50d5170f304cc
22.3 MB Preview Download

Additional details

Related works

Is supplement to
https://github.com/SysBioChalmers/GECKO/tree/v3.0.0 (URL)