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Releases: SysBioChalmers/EnzymeConstrained_humanModels

An enzyme-constrained model of Human metabolism

16 May 15:44
@IVANDOMENZAIN IVANDOMENZAIN
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An enzyme-constrained model of Human metabolism Pre-release
Pre-release

Code and files for reproducibility of the simulation results section An enzyme-constrained model of Human metabolism for the paper manuscript: "An Atlas of Human Metabolism"

This repository serves as a toolbox that allows the enhancement of a humanGEM based model with enzyme constraints with the use of the GECKO toolbox. It also contains several scripts and functions for simulation purposes with ecModels of human metabolism:

  • setEMEMmedium: Sets Eagle's minimum medium constraints for a cell-line specific ecModel.
  • comparativeFVA_humanModels: Performs a simultaneous FVA on a cell-line specific model and its enzyme-constrained counterpart.
  • essentiallityAnalysis: Performs gene essentiallity analysis for a human metabolism model (for both GEMs and ecModels).

The script generate_human_ecModels_NCI60.m generates the 11 cell-line NCI60 ecModels used for this study and the function ExchFluxesComparison_NCI60.m performs the FBA simulations and comparisons with experimental data for exchange fluxes and growth rates that are included in the paper manuscript.

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