liver-model-manuscript
QSP model of liver lipid metabolism for 2022 publication.
Science Score: 54.0%
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✓CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.4%) to scientific vocabulary
Last synced: 6 months ago
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Repository
QSP model of liver lipid metabolism for 2022 publication.
Basic Info
- Host: GitHub
- Owner: openPfizer
- License: apache-2.0
- Language: Julia
- Default Branch: main
- Size: 1.22 MB
Statistics
- Stars: 6
- Watchers: 0
- Forks: 2
- Open Issues: 0
- Releases: 2
Created almost 4 years ago
· Last pushed over 3 years ago
Metadata Files
Readme
License
Citation
README.md
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 generateparameters_pluto.csv- Default parameter file, written by executingderived_parameters.jlbased on initial seeding fromparameters.xlsx. The values in this file are the ones that are used inmain.jlby default.parameters.xlsx- Parameter file template that is the input toderived_parameters.jlchange 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 modellit_std_sim.jl- Script for deriving some values from digitized literature. Not essential for program execution.lognormal_util.jl- Useful functions for litstdsim.jl. Not essential for program execution.mh_sim.jl- Function for simulating and scoring the model within the Metropolis-Hastingsmh.jl- Main Metropolis-Hastings function used for generating plausible patients.select_vps- Acceptance/rejection sampling of plausible patients to virtual patientsutil.jl- Some shorter, misc. functions that were needed.
Owner
- Name: openPfizer
- Login: openPfizer
- Kind: organization
- Repositories: 1
- Profile: https://github.com/openPfizer
Coding together for a healthier world
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: Source Code for the Liver Lipid Metabolism Model
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Theodore R. Rieger
family-names: Rieger
name-particle: Theodore
email: ted.rieger@pfizer.com
affiliation: Pfizer Inc
orcid: 'https://orcid.org/0000-0002-9610-0983'
- given-names: Richard J. Allen
name-particle: Richard
family-names: Allen
affiliation: Pfizer Inc
- given-names: C.J. Musante
name-particle: C.J.
family-names: Musante
affiliation: Pfizer Inc
identifiers:
- type: url
value: >-
https://github.com/openPfizer/Liver-Model-Manuscript
description: GitHub repository for the source code.
- type: doi
value: 10.5281/zenodo.6621096
description: Zenodo DOI for the most recent release.
repository-code: >-
https://github.com/openPfizer/Liver-Model-Manuscript
abstract: >-
Source code accompanying Rieger et al. manuscript
on liver lipid metabolism. This software will
reproduce all the results in the manuscript.
keywords:
- NAFLD
- QSP
- Mathematical Model
- Virtual Patient
- NASH
- Metabolic Syndrome
license: Apache-2.0
version: v1.1
date-released: '2022-06-07'