GECKO 3.0.2

[edkerk]

Main improvements in this PR:

• Documentation:
  • Clarifications and fixes in protocol.m (solves Minor enhancement in protocol.m #279, Error in minimizing protein pool usage #287).
  • Protein concentrations (in model.ec.concs and proteomics data) are in mg/gDCW.
• Fix:
  • Correct calculation of new protein pool if constrained with proteomics, by considering the total amount of measured protein.
  • getStandardKcat can use data/pseudoRxns.tsv as input of reactions to ignore, it overwrites previous standard Kcat definitions, and specifies model.ec.source{i} = 'standard' if a standard kcat is assigned to a zero-kcat reaction (solves getStandardKcat assigns protein costs to pseudo-reactions #280, ec.source in getStandardKcat #286)
  • Various bugfixes in fuzzyKcatMatching (solves Bug: Looks for the taxonomically closest organism for matching the Kcats #277), readDLKcatOutput (solves Bug: check if DLKcat.tsv has actually been run through DLKcat #278), getECfromDatabase (solves Bug detected getECfromDatabase #281), sensitivityTuning (solves New feature sensitivityTuning #285), & applyCustomKcats (solves Error in matching the custom Kcats #291).

I hereby confirm that I have:

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

[github-actions]

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

 
Running geckoCoreFunctionTests
Model-specific DLKcat input stored at /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/ecTestGEM/data/DLKcat_input_test.tsv
Limit has been reached. Protein P5 seems to be problematic. Consider changing the kcat.
Done geckoCoreFunctionTests
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Note: In the case of multiple test runs, this post will be edited.