Compiled SBML models from PEtab yaml file
The SOP creates a separate SBML model for each drug and condition, as the PEtab problem contains diffrent experimental data for them.
However, the SBML models only differ in their name as for all drugs and conditions, the same exponential decay model was assumed.
The SBMLs are automatically created by yaml2sbml, when the SOP is executed. Therefore, these files are for completeness only and are not necessary to replicate the analysis.
SEEK ID: https://fairdomhub.org/models/819?version=1
1 item is associated with this Model:-
SBML models.zip (Zip file - 17.7 KB)
Organism: Mus musculus
Model type: Ordinary differential equations (ODE)
Model format: SBML
Execution or visualisation environment: Not specified
Model image: No image specified
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Created: 22nd Jul 2022 at 08:11
Last updated: 9th Dec 2022 at 06:08
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Version 2 (latest) Created 7th Dec 2022 at 16:08 by Sebastian Höpfl
Increased sample size to 200,000 on 4 parallel chains. Increased bounds of parameters to a uniform prior distribution in the interval [0, 100] for parameters A and B and [0,1000] for σ.
Version 1 (earliest) Created 22nd Jul 2022 at 08:12 by Sebastian Höpfl
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Projects: Working Group Nicole Radde, SteaPKMod
Institutions: University of Stuttgart
https://orcid.org/0000-0002-5300-0915
Currently I focuse on the integration of data into multi-scale models with statistical methods and uncertainty tracking in the research unit QuaLiPerF.
Projects: SteaPKMod
Web page: https://www.uniklinikum-jena.de/avc/Forschung/Experimentelle+Chirurgie.html
The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...
Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, SABIO-VIS
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The group around Nicole Radde specializes in the modeling, analysis, and simulation of biochemical systems. This especially includes parameter optimization and identification.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: https://www.ist.uni-stuttgart.de/research/group-of-nicole-radde/
Start date: 11th Feb 2020
Investigation regarding the impact of periportal steatosis on selected parameters of drug metabolism.
Programme: Experimental Transplantation Surgery
Public web page: https://qualiperf.de/
Submitter: Uta Dahmen
Investigation: 1 hidden item
Assays: Animal experiment and Pharmacokinetics data, Bayesian uncertainty quantification, Hematoxylin-Eosin (HE) staining, Immunohistochemistry _ CYP1A2, Immunohistochemistry _ CYP2D6, Immunohistochemistry _ CYP2E1, Immunohistochemistry _ CYP3A4, SteaPk-data Histology Quant., CYP activity, Protein, TG, AUC
The experimental data of Midazolam, OH-Midazolam, Caffein, Codeine, Norcodeine, Codein-6Glucuronide, Morphine-3Glucuronide and Morphine was analyzed via a Bayesian uncertainty quantification. An underlying model describing the bolus injection, followed by the exponential decay was written in sbml and a PEtab problem was created. The sampling and ensemble creation was conducted with the python toolbox pyPESTO.
For further details, please take a look at the methods section of the paper.
Submitter: Sebastian Höpfl
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
The experimental data of Midazolam, OH-Midazolam, Caffein, Codeine, Norcodeine, Codein-6Glucuronide, Morphine-3Glucuronide and Morphine was analyzed via a Bayesian uncertainty quantification. An underlying model describing the bolus injection, followed by the exponential decay was written in sbml and a PEtab problem was created. The sampling and ensemble creation was conducted with the python toolbox pyPESTO.
For further details, please take a look at the methods section of the paper.
Submitter: Sebastian Höpfl
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
