GECKO 3.1.0

[edkerk]

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.

I hereby confirm that I have:

• [x] Selected main as a target branch (top left drop-down menu)

[edkerk]

Suggestion version bump to 3.1.0 due to large number of changes and broken reverse compatibility due to changed parameter names etc.

[github-actions[bot]]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
Running geckoCoreFunctionTests
Done geckoCoreFunctionTests
__________

Note: In the case of multiple test runs, this post will be edited.