Liver-Model-Manuscript

QSP model of liver lipid metabolism for 2022 publication.

Most Recent Release

Execution

• setup.jl - Will initialize the project, this step can be slow, especially the first time, hence we have split it from the main script.
• main.jl - Main project script, executing this script will generate the figures from the manuscript.

Input Files

• run_paramaters.csv - Key parameters for controlling a run of the model, including fit flags and the number of plausible patients to generate
• parameters_pluto.csv - Default parameter file, written by executing derived_parameters.jl based on initial seeding from parameters.xlsx. The values in this file are the ones that are used in main.jl by default.
• parameters.xlsx - Parameter file template that is the input to derived_parameters.jl change this file if adding new parameters to the model.

Additional Functions

• derived_parameters.jl - Pluto notebook where we derived some of the baseline parameter values from the model. Load by launching Pluto and opening this notebook.
• dxdt.jl - ODEs of the model
• lit_std_sim.jl - Script for deriving some values from digitized literature. Not essential for program execution.
• lognormal_util.jl - Useful functions for lit_std_sim.jl. Not essential for program execution.
• mh_sim.jl - Function for simulating and scoring the model within the Metropolis-Hastings
• mh.jl - Main Metropolis-Hastings function used for generating plausible patients.
• select_vps - Acceptance/rejection sampling of plausible patients to virtual patients
• util.jl - Some shorter, misc. functions that were needed.