odendaal2 Version 1
Simulate Model on Copasi
Simulate Model on JWSAdjusted model to test the model's ability to oxygen consumption rate by permeabilised HepG2 cells in an Oroboros oxygraph. Data from Fletcher et al. (2019).
SEEK ID: https://fairdomhub.org/models/833?version=1
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odendaal2.xml (XML document - 638 KB)
Organism: Homo sapiens
Model type: Ordinary differential equations (ODE)
Model format: SBML
Execution or visualisation environment: JWS Online
Model image: No image specified
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Views: 911 Downloads: 50 Runs: 3
Created: 23rd Feb 2023 at 14:44
Last updated: 13th Jun 2023 at 14:53
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Version 1 (earliest) Created 23rd Feb 2023 at 14:44 by Christoff Odendaal
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https://orcid.org/0000-0001-6274-3633I am a Professor in Medical Systems Biology and the University Medical Centre Groningen. The research in my lab is focused on complex regulation of mammalian lipid and carbohydrate metabolism, eventually aiming at network-based therapies. We combine dynamic computer simulations with quantitative metabolomics, 13C fluxomics, proteomics and transcriptome analysis, and in depth biochemical analysis. This allows to predict and understand ‘emergent’ properties, those properties that are counterintuitive ...
Projects: PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University of Leiden
Projects: PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University Medical Centre Groningen
PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.
Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease ...
Programme: This Project is not associated with a Programme
Public web page: http://polimer-itn.eu/
Submitter: Christoff Odendaal
Studies: Model analysis, Model construction, Model validation, Sequestration of CoA and adaptation of CoA metabolism in MCAD-knockout c...
Assays: ACAD activity partitioning, Comparing acyl-CoA dehydrogenase deficiencies, Computational model (in silico), HepG2 cells (in vitro), HepG2 oxygen consumption, Kinetics Minireviews, MCADD patient personalised modelling, MCADD rescue titration, Metabolic control analysis, Mice (in vivo), Models, Predicting urinary acylcarnitines under metabolic decompensation., Whole-body ketogenic flux
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Kinetics Minireviews, Models
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: ACAD activity partitioning, HepG2 oxygen consumption, Whole-body ketogenic flux
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model construction
Validation of model's ability to predict oxygen consumption flux as measured usign permeabilised cells in an Oroboros Oxygraph. Generates Fig. 2A in the associated publication.
Download "Model_notebooks.rar", unzip, and run: "2, generate-model-Oroboros-validation-[needs(1)]-20221109.nb" and "4, Fig2A-Oroboros-simulation-data-[needs-(1-2-and-3)]-20221109.nb" after running "1, generate-model-20221109.nb"
Submitter: Christoff Odendaal
Biological problem addressed: Validation
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model validation
