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GECKO v1.2.0
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@BenjaSanchez BenjaSanchez released this 12 Apr 06:51
v1.2.0
5b1ef84
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Learn about vigilant mode.
  • Implemented automatic kcat flexibilization for over-constrained models:
    • Based on a maximum growth rate specified by the user, the algorithm iteratively identifies the top growth-limiting kcat value and changes it for the highest one in BRENDA (same EC number)
    • Once that the model is growing close to the set value, the average enzyme saturation factor is refitted
    • For non-feasible/zero-growth models, sensitivity analysis is performed on a reaction and enzyme basis rather than on individual kcat values
    • The outputs of this step are stored in topUsedEnzymes.txt and kcatModification.txt and can be used for further manual curation
  • All databases updated (BRENDA, swissprot, KEGG, PaxDB)
  • More generic gene/protein matching for compatibility with other models
  • Re-organization of all output files in a single folder
  • New badges + styling of website

NOTE: Also not available in pypi (issue #14 still unresolved)

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