Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: sciencedirect.com -
○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 (10.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: rivm-syso
- License: eupl-1.2
- Language: Jupyter Notebook
- Default Branch: main
- Size: 39.9 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
PFAS PBK model
This repository contains the source code of a PFAS PBK model implementation based on the PFOA and PFOS PBK model by Loccisano et al. (2011) and the subsequently modified version thereof by Westerhout et al. (2024). The model is implemented in Antimony and available as an annotated SBML file compliant with the FAIR PBK standard.
Model code
The model code can be found in the model folder. The file PBK_PFAS.ant contains the Antimony implementation. The file PBK_PFAS.csv contains the unit specifications and the model element annotations according the FAIR PBK standard, using the harmonized terminology of the PBPKO ontology. The file PBK_PFAS.sbml is generated automatically from the model code and annotations file using the SBML PBK workflow. This generated SBML file is the interoperable and reusable digital resource of this model implementation.
Demonstration of use
The Jupyter notebook test_dosing.ipynb demonstrates how this model can be used in simulations.
Running the notebooks
To run the notebooks, you need Python with Jupyter Notebook and the python packages listed in the requirements file. Install notebook and the required python packages using the command:
pip install -r requirements.txt
Owner
- Name: Rijksinstituut voor Volksgezondheid en Milieu
- Login: rivm-syso
- Kind: organization
- Email: info@rivm.nl
- Location: Bilthoven, The Netherlands
- Website: www.rivm.nl
- Repositories: 13
- Profile: https://github.com/rivm-syso
Citation (CITATION.cff)
cff-version: 1.2.0
title: PFAS PBK model
abstract: FAIR PFAS PBK model implementation in Antimony and SBML.
version: 0.1.0
authors:
- family-names: Minnema
given-names: Jordi
orcid: "0000-0002-1847-4218"
affiliation: RIVM
- family-names: Westerhout
given-names: Joost
orcid: "0000-0001-9068-0916"
affiliation: RIVM
- family-names: Kruisselbrink
given-names: Johannes
affiliation: WUR
orcid: "0000-0003-1673-5725"
GitHub Events
Total
- Push event: 4
Last Year
- Push event: 4
Dependencies
- actions/checkout v4 composite
- actions/setup-python v4 composite
- antimony >=2.15.0
- jupyter >=1.1.1
- nbconvert >=7.16.6
- pandas ==2.2.2
- parameterized >=0.9.0
- python-libsbml >=5.20.5
- sbmlutils >=0.9.0
- seaborn >=0.13.2
- tellurium >=2.2.10