Models

What is a Model?
413 Models visible to you, out of a total of 656

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

No description specified
No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

No description specified
No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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

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

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

Human mitochondrial fatty acid oxidation of saturated, even chain acyl-Coas beginning at C16. See Model description for detail.

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.

No description specified

Creator: Vincent Wagner

Submitter: Vincent Wagner

No description specified

Creator: Vincent Wagner

Submitter: Vincent Wagner

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

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

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

No description specified

Creator: Vincent Wagner

Submitter: Vincent Wagner

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

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

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 ...

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

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

Powered by
(v.1.14.0-pre)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH