Models
What is a Model?Filters
This folder contains the python code for developing weighted loss trainer (WeLT) with all the expiremnatal work. Here is the link for our public [GitHub repository] (https://github.com/mobashgr/WELT.git).
Creator: Ghadeer Mobasher
Submitter: Ghadeer Mobasher
Model type: Not specified
Model format: Python code
Environment: Not specified
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
The FEM models how metabolic slowdown will induce the age-related changes of weight gain, insulin resistance, basal inflammation, mitochondrial dysfunction, as well as the age-related disease of atherosclerosis, via a series of unavoidable homeostatic shifts.
Creators: James Wordsworth, Pernille Yde Nielsen
Submitter: James Wordsworth
Model type: Ordinary differential equations (ODE)
Model format: R package
Environment: Not specified
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Underlying R script for the investigation of immune cells. Script contains basic data processing, as well as a DE and monocle analysis.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Adjusted 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).
Creators: Christoff Odendaal, Emmalie Jager, Terry G.J. Derks, Barbara Bakker
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Adjusted model to test the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Data from Aoyama et al. (1995).
Creators: Christoff Odendaal, Barbara Bakker, Emmalie Jager, Terry G.J. Derks
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Human mitochondrial fatty acid oxidation of saturated, even chain acyl-Coas beginning at C16. See Model description for detail.
Creators: Christoff Odendaal, Emmalie Jager, Barbara Bakker, Terry G.J. Derks
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Unzip model notebooks and keep in the same folder. Notebook names state which notebooks need to be run before them in order for them to word, e.g. "[needs-(1)]" indicates that the notebook numbered 1 must be run and its exported output generated before the given notebook can work. This has to do with the model being generated in only one notebook to avoid duplication.
Creators: Christoff Odendaal, Barbara Bakker, Emmalie Jager, Terry G.J. Derks
Submitter: Christoff Odendaal
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Not specified
Model format: Not specified
Environment: Not specified
The folder contains the jupyter notebook for the execution of all analyses of the study. The BEST method is used in the notebook and is added in a separate python skript.
There is a class for the BEST method according to Kruschke and a class für the BEST multiple comparison.
A conda environment file with all libraries that are necessary to perform the analysis, including the package version was created. It can be easily installed via conda env create -f pymc_env.yml
Creator: Sebastian Höpfl
Submitter: Sebastian Höpfl
Model type: Not specified
Model format: Not specified
Environment: Not specified
The exponential decay model with all parameters, observables and conditions was specified in a yaml file.
This yaml file is converted with yaml2sbml (2020 Jakob Vanhoefer, Marta R. A. Matos, Dilan Pathirana, Yannik Schaelte and Jan Hasenauer) to a PEtab problem, which contains also the SBML model.
Creator: Sebastian Höpfl
Submitter: Sebastian Höpfl
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
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.
Creator: Sebastian Höpfl
Submitter: Sebastian Höpfl
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Not specified
Model format: Not specified
Environment: Not specified
Stoichiometric model in SBML format using the acetate-aerobic standard scenario.
Please note that SBML was exported using the sbmlwriter class of Metano. This file was not used for the actual analyses.
Creator: Julia Koblitz
Submitter: Julia Koblitz
Model type: Stoichiometric model
Model format: SBML
Environment: Not specified
This stoichiometric model of Aromatoleum aromaticum EbN1 is a genome-scale model and comprises 655 enzyme-catalyzed reactions and 731 distinct metabolites.
The model is in the plain-text reaction format of Metano that is human-readable and can be opened with every text editor. To run this version of the model, please use the Metano Modeling Toolbox (mmtb.brenda-enzymes.org) and the associated scenario files.
Creators: Julia Koblitz, Dietmar Schomburg, Meina Neumann-Schaal
Submitter: Julia Koblitz
Model type: Stoichiometric model
Model format: Not specified
Environment: Not specified
Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species ...
Creators: Maksim Zakhartsev, Filip Rotnes, Marie Gulla, Ove Oyas, Jesse van Dam, Maria Suarez Diez, Fabian Grammes, Wout van Helvoirt, Jasper Koehorst, Peter Schaap, Yang Jin, Liv Torunn Mydland, Arne Gjuvsland, Sandve Simen, Vitor Martins dos Santos, Jon Olav Vik
Submitter: Jon Olav Vik
Model type: Stoichiometric model
Model format: SBML
Environment: Not specified
A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover", J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2". The other model variants are all available from www.plasmo.ed.ac.uk as stated in the publication. Note that the 'P2011' circadian clock model was modified for this publication (as described), in order to replicate the ...
Creators: Andrew Millar, Daniel Seaton
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Matlab model (could not be represented in SBML) from publication with abstract: Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription. ...
Creators: Andrew Millar, Daniel Seaton
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Matlab