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Model provenance

ecYeastGEM.yml

The full enzyme-constrained yeast model, in GECKO 4 / RAVEN 3 YAML format.
Source SysBioChalmers/ecModels, ecYeastGEM/models/ecYeastGEM.yml
Branch gecko4
Commit 880288747ad98220764ce07f8b7a396048e0537d
Blob d684eb01ddaf49da9ac9f5891aae372e16b34542
Base model yeast-GEM 9.1.1
Built with geckopy 4.0.0b1

1144 enzymes over 4850 enzyme-constrained reactions. The kcats were tuned against measured growth rates and exchange fluxes with CMA-ES, see the ecYeastGEM README in the source repository.

The model ships with r_4046 (non-growth associated maintenance) pinned at 0.7 mmol ATP/gDW/h and prot_pool_exchange bounded at 125 mg/gDW, which is p_tot * f * sigma * 1000 for the distributed defaults. Both are replaced per condition when building the proteome-constrained models.

yeast-GEM.yml

The conventional GEM the ecModel was built from, yeast-GEM release v9.1.1 (model/yeast-GEM.yml, sha256 2ddfaaa73ead41ab243127d1b34fa56db2c86052f6eabcd12bb4eea93947dc17). Used as conv_gem by the geckopy adapter and as the starting model for random sampling.

Verifying

curl -sL https://raw.githubusercontent.com/SysBioChalmers/ecModels/880288747ad98220764ce07f8b7a396048e0537d/ecYeastGEM/models/ecYeastGEM.yml \
  | git hash-object --stdin
# d684eb01ddaf49da9ac9f5891aae372e16b34542
curl -sL https://raw.githubusercontent.com/SysBioChalmers/yeast-GEM/v9.1.1/model/yeast-GEM.yml | sha256sum