Releases: SysBioChalmers/EnzymeConstrained_humanModels
Releases · SysBioChalmers/EnzymeConstrained_humanModels
An enzyme-constrained model of Human metabolism
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 bothGEMs
andecModels
).
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.