Simulation Toolbox for Infant Growth with focus on Metabolism.
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readme.md

Simulation Toolbox for Infant Growth with focus on Metabolism (STIG-met)

  • STIG-met is an integrated platform for simulation of human growth. We combine the experience from traditional growth models with GEMs to provide predictions of metabolic fluxes with enzyme level resolution on a day-to-day basis.

  • Abstract:

An estimated 165 million children globally have stunted growth, and extensive growth data are available. Genome scale metabolic models allow the simulation of molecular flux over each metabolic enzyme, and are well adapted to analyze biological systems. We used a human genome scale metabolic model to simulate the mechanisms of growth and integrate data about breast-milk intake and composition with the infant’s biomass and energy expenditure of major organs. The model predicted daily metabolic fluxes from birth to age 6 months, and accurately reproduced standard growth curves and changes in body composition. The model corroborates the finding that essential amino and fatty acids do not limit growth, but that energy is the main growth limiting factor. Disruptions to the supply and demand of energy markedly affected the predicted growth, indicating that elevated energy expenditure may be detrimental. The model was used to simulate the metabolic effect of mineral deficiencies, and showed the greatest growth reduction for deficiencies in copper, iron, and magnesium ions which affect energy production through oxidative phosphorylation. The model and simulation method were integrated to a platform and shared with the research community. The growth model constitutes another step towards the complete representation of human metabolism, and may further help improve the understanding of the mechanisms underlying stunting.

  • KeyWords:

Utilisation: maximising growth, predictive simulation, experimental data reconstruction; Model Source: HMR2.00; Taxonomy: Homo sapiens Condition: Malnourishment, Starvation,

This repository is administered by name @avlant, Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology

Installation

Required Software:

  • PROGRAMMING LANGUAGE/Version (e.g.):
    • You need a functional Matlab installation of Matlab_R_2015_b (MATLAB 7.3 and higher)
    • The RAVEN toolbox for MATLAB. Add the directory to your Matlab path, instructions here

Run

To reproduce figure 1 run main.m. For other figures run main[name of simulation].m

Aditional information

For a visual guide to the structure of the simulation toolbox, view readme.pptx

License

This work is licensed under a Creative Commons Attribution- NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http:// creativecommons.org/licenses/by-nc-sa/4.0/