Models

Unzip model notebooks and keep in the same folder. Notebook "0, generate_model.nb" needs to be run before the others can be, as the model needs to be exported as Excel files before they cvan be used to make the figures.

This is the brusselator model from the COPASI distribution

Please see the Readme file for information regarding the simulation enivronment and file contents.

Parameters rescaled and scaling factors set to 1

This is the scaled version of U2020.4 in sbml file. It already contains the scaling factors

Paramters rescaled and scaling factors set to 1

Paramteres rescaled and scaling factors set to 1

Parameters rescaled and scaling factors set to 1

Derived from U2019.3 from Testing the inferred rate of dynamic, gene regulatory network in absolute units

Sbml version of U2019.4 with reacaling factors values already incoporated in the model. This was generated autmatically using tellurium python package

This file was derived from U2020.3 by introducing the scalig factors in the required locations in the model. This files is used then for numerically rescaling the model for matching synthetic protein data.

We recommend to use a virtual environment with a python 3.11 distribution to reproduce our results. Using anaconda and the environment file eulerpi_env.yml, the working virtual environment is set up through the prompt

conda env create -f eulerpi_env.yml

The environment file eulerpi_env.yml contains a human-readable list of all required dependencies. Consequently, these dependencies can also be installed manually.

In addition to this README and the environment file, the downloaded .zip ...

HSD11B1 inhibition by AZD4017 and the effect on cortisone and 11KA4 metabolism was simulated in Mathematica. Figure 6 of the manuscript is reproduced in the notebook.

Mathematica notebook for simulation of combined effect of HSD11B1/AKR1C3 ratio variation and HSD11B1 inhibition, surface plots are generated shown in Fig. 4 of the manuscript.

HSD11B1 was inhibited by CBX and the effect on cortisone and 11KA4 conversion was simulated. Model simulated in Mathematica, Figure 3 panels are presented.

Mathematic notebook for enzyme kinetic analysis and model fit, including figure generation for manuscript.

Mathematica notebook with model simulation of metabolite profiles after 24h incubation with different ratios of HSD11B1 and AKR1C3 transfected HEK293 cells.

First version of Genome-scale metabolic model (GEM) for reconstraction of flavonoids biosynthetic pathways. This model includes as a chassis , the Pseudomonas Putida GEM (iJN1411) . It includes the metabolic reconstruction of more than 500 flavonoids and more than 500 reactions related to the flavonoid biosynthesis.

This folder contains the python code for developing weighted loss trainer (WeLT) with all the expiremnatal work. Here is the link for our public [GitHub repository] (https://github.com/mobashgr/WELT.git).

The FEM models how metabolic slowdown will induce the age-related changes of weight gain, insulin resistance, basal inflammation, mitochondrial dysfunction, as well as the age-related disease of atherosclerosis, via a series of unavoidable homeostatic shifts.