GECKO 3.2.1

• Fixes:
  • getStandardKcat.m removed enzymes when it was run on a model already containing standard kcat values
  • ecFVA will swap min and max values the reaction directionality was swapped when mapping from ec- to conventional model
  • plotEcFVA will use its own cdfplot function, to avoid dependency on MATLAB Statistics and Machine Learning Toolbox. Blocked reactions are excluded from the graph. ⚠️ The plot in full_ecModel shows minor differences, also due to code changes introduced by GECKO 3.2.0
• Features:
  • calculateFfactor can handle protData with multiple conditions (in which case, averages over all conditions are taken)
  • setKcatForReactions allows multiple kcat values as input, allowing to set kcat of multiple reactions at the same time
  • reportEnzymeUsage will report both the summed usage of isoenzymes, as well as the individual usage of the separate reactions. topUsage and highCapUsage outputs columns are harmonized
  • constrainFluxData if a provided constraint is either -1000 or 1000, lower and upper bound will be constraint to either uptake or excretion only, irrespective of what option is given as the looseStrictFlux parameter
  • constrainEnzConcs can also remove enzyme concentration constraints
• Refactor:
  • fuzzyKcatMatching to avoid warnings "Colon operands must be real scalars" in recent MATLAB versions
• Documentation:
  • various function documentations, warnings and error messages have been improved