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GECKO 3.1.0
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@edkerk edkerk released this 03 Jul 15:17
· 78 commits to main since this release
v3.1.0
6378555
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Learn about vigilant mode.

Main improvements in this PR:

  • Features:

    • Renamed various parameters in model adapter.
    • getComplexData uses taxonomic ID instead of species name.
    • GECKOInstaller checks if correct RAVEN version is installed (release 2.8.3+).
    • Tutorials are moved to tutorials, and userData is removed as default location for model files. Users are encouraged to make their model folders outside the GECKO directory, facilitated by startGECKOproject().
    • full_ecModel tutorial:
      • more detailed discussions around kcat curation, protein usage etc.
      • plotCrabtree makes plot that demonstrates Crabtree effect in ecModels
      • plotlightVSfull makes plot comparing flux distribution in light and full ecModels
    • light_ecModel:
      • minimum code to make a light ecModel based on human-GEM 1.15.0
      • make contextualized ecModel based on a cell-line specific tINIT model with getSubsetEcModel
    • ecFSEOF is compatible with GECKO3.
    • makeEcModel can use pseudoRxns.tsv to filter out pseudoreactions.
    • various functions show progress bar that indicates estimated remaining time.
    • reportEnzymeUsage can make report of top-10 used enzymes.
    • loadConventionalGEM can load yaml model files.
    • enzymeUsage reports as positive values.
    • flexibilizeProtConcs also keeps track of the ratio of protein concentration change.
    • fillProtConcs allows for selection of column from protData, if it contains multiple datasets.
    • setKcatForReactions can directly modify a kcat for all associated reactions, useful for manual curation on existing ecModels.
    • getReactionsFromEnzyme gives which reactions are catalyzed by a particular enzyme, from a provided Uniprot ID.
    • copyECtoGEM to copy ecModel.ec.eccodes to ecModel.eccodes.

  • Documentation:

    • All function documentation is available from /doc/ and online (becomes available upon PR commit).
    • sensitivityTuning allows for ignoring selected reactions.

  • Fix / refactor:

    • Numerous fixes and refactoring of code in many functions.
    • Note that various functions have had their input parameters changed.
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