GECKO v1.2.1

• Features:
  • All genes from the original yeast model now included in the .xml file. Genes connected to enzyme constraints are now stored in model.enzGenes in the .mat structure.
  • Docs badge in README.
• Fixes:
  • Fields grRules and rules fixed in a consistent way:
    • grRules for the backwards reactions are the same as for the forward ones.
    • For reactions catalyzed by just 1 enzyme (or complex), grRules of the original reactions are assigned to them.
    • For reactions catalyzed by more than 1 enzyme (or more than 1 complex), grRules of the original reactions are assigned to the arm reactions, and the corresponding sub-rules are assigned to the isozyme-controlled reactions.
    • For enzyme exchange reactions, grRules are assigned as the corresponding gene ID.
    • The rules field is set equal to grRules for providing consistency with different toolboxes.
  • Inter-OS compatibility:
    • Numbers in scientific notation are stored in the .xml files with format Xe-0N, not Xe-00N, or with format Xe-1N, not Xe-01N, regardless of the OS used for generating them.
    • Numbers in all files are shown with up to 6 significant figures.
• Refactoring:
  • Updated to new COBRA standards for addReaction usage.

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

GECKO v1.2.0

• 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)

GECKO v1.1.2

• Improved kcat matching to BRENDA with:
  1. Specific activity
  2. Phylogenetic distance, when data for organism of choice is not available
• Switched to readthedocs for documentation: http://geckotoolbox.readthedocs.io
• Added a Gitter room for discussion: https://gitter.im/SysBioChalmers/GECKO
• Switched to a simplified GitFlow structure (master + devel + feature branches)
• Python 3.4 environment dropped in CI (no longer supported by pandas)

NOTE: Failing some tests in Travis (issue #14 unresolved), i.e. not available in pypi

GECKO v1.1.1

• GECKOpy now deploys to PyPI: https://pypi.python.org/pypi/geckopy
• Removed MAC builds from Travis
• Changed license to a generic MIT one
• Reformatted readme file to .rst for PyPI compatibility
• Added contributors

GECKO v1.1.0

Main new things:

• Added GECKOpy
• Improved matching criteria
• Made SBML files compliant to current standards
• Published website: https://sysbiochalmers.github.io/GECKO/
• A bunch of bugs fixed
• Updated databases

GECKO v1.0.0

This is the first release of GECKO in Github. Both GECKO and ecYeast7 in this release were used for all results presented in the published paper of the software. Usage instructions can be found in the README.md file.