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Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.

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Enzyme-constrained Human1 GEMs

This directory contains an automated pipeline for constructing cell-specific enzyme-constrained GEMs (ecGEMs) derived from Human-GEM (v1.3.0) based on transcriptomics and proteomics datasets.

Required Software:

Dependencies - Recommended Software:

Regenerating the ecGEMs:

The ecGEMs are already present in the models/ subdirectory, but the scripts and data necessary to regenerate the models are available here. The master script for generating the ecGEMs from the tINIT GEMs (provided in the /models/humanGEM_cellLines/11models.mat file) is generate_human_ecModels_NCI60.m, located in the /ComplementaryScripts directory. Run this generate_human_ecModels_NCI60 script in MATLAB to regenerate the 11 ecGEMs.

Flux variability analysis

Flux variability analysis (FVA) (corresponding to the results presented in Fig. 5B) can be run using the comparativeFVA_humanModels.m function in the ComplementaryScripts/Simulation subdirectory. Specify the name of the model (cell line) for which FVA is to be run; for example:

results = comparativeFVA_humanModels('HOP62');

Prediction of growth and metabolite exchange rates:

To use the ecGEMs and non-ecGEMs to predict growth rates and metabolite exchange rates with increasing levels of constraints (as shown in Figs. 5C and 5D), run the predict_cellLines_gRates.m script in the ComplementaryScripts subdirectory.

Generating plots for Figure 5

The R script used to generate plots shown in Fig. 5 of the main text is plot_ecGEM_results.R, located in the ComplementaryScripts subdirectory.

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Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.

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