Models

What is a Model?
418 Models visible to you, out of a total of 662

Interactions of the SARS-CoV-2 E protein with human proteins in the context of histone acetylation.

Creator: Francesco Messina

Submitter: Marek Ostaszewski

E.coli Core model, with additional reactions added to generate the beta-oxadation cycle. This is the basic model used in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).

Creator: Natalie Stanford

Submitter: Natalie Stanford

A model of E. coli central carbon core metabolism, used as starting point for B. subtilis modelling. It is developed by Chassagnole et al. doi:10.1002/bit.10288.

Creators: Ulf Liebal, Fei He

Submitter: Ulf Liebal

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

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

First version of enzyme-constrained model (ecModel) for Pseudomonas putida KT2440

Creator: Cheewin Kittikunapong

Submitter: Cheewin Kittikunapong

First version of enzyme-constrained model (ecModel) for Escherichia coli

Creator: Cheewin Kittikunapong

Submitter: Cheewin Kittikunapong

First version of enzyme-constrained model (ecModel) for Streptomyces albus J1074

Creator: Cheewin Kittikunapong

Submitter: Cheewin Kittikunapong

The mechanisms of the Electron Transport Chain under COVID-19, including Nsp7, Nsp8 and Orf9c

Creator: Julia Scheel

Submitter: Marek Ostaszewski

Mathematica notebook for the parameterisation of the ENO rate equation based on SEEK linked experimental data.

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

A minimal model showing the core of resource allocation models as it can either be invested in enzymatic machinery or single biomass components with the best yield. The model is written in SBML using the RAM extension for use in deFBA. Compatible python software for simulation can be found at https://tinyurl.com/yy8xu4v7

Creator: Henning Lindhorst

Submitter: Henning Lindhorst

SARS-CoV-2 impact on the ER stress

Creators: Cristobal Monraz, Inna Kuperstein, Barbara Brauner

Submitter: Marek Ostaszewski

This function estimates the parameters of growth functions of the acid-forming and solvent-forming population observed in 'forward'-shift experiments of phosphate-limited continuous cultures of C. acetobutylicum. The parameters are used in the 'Two-Populations'-Model of the pH-induced metabolic shift.

It assumed that the found behaviour of the optical density during these experiments results from a phenotypic switch caused by the changing pH level.

Creator: Thomas Millat

Submitter: Thomas Millat

Python scripts to run the analysis estimating rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.

Creators: Daniel Seaton, Andrew Millar

Submitter: Daniel Seaton

Before running the code, please install eulerpi (via pip install eulerpi).

The .zip file contains 5 individual python files and a Data folder that includes all data used for inference. Three of the files are named *plot.py and can be used to reproduce the plots of our article for one respective example model. To this end, the files contain several function definitions and an executable part at the end. The *plot.py files can be executed and produce (Sub-)Figures that are saved in the ...

Creator: Vincent Wagner

Submitter: Vincent Wagner

A population of turtles have between 1 and 3 genes contributing to the strength of selective destruction, which can either cause ageing or allow for negligible senescence.

Creator: James Wordsworth

Submitter: James Wordsworth

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

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