Models

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

Originally submitted model file for PLaSMo accession ID PLM_1, version 1

Creators: BioData SynthSys, Chris Davey

Submitter: BioData SynthSys

This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.

Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. ...

Creators: Hans V. Westerhoff, Raju Prasad Sharma, Alexey Kolodkin

Submitter: Hans V. Westerhoff

RUN the model for steady state.

For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. Plot e.g. ATP.

For H2O2 experimental data validation for repeated treatment at 50uM, 150uM, and 300uM. To run the model with different dosing scenarios, one has to set both the H2O2 initial ...

Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma

Submitter: Alexey Kolodkin

This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.

Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. ...

Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma

Submitter: Alexey Kolodkin

A small model representing the core carbon network in each cell. For more detail on the model creation see [1]. 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

[1] S. Waldherr, D. A. Oyarzún, A. Bockmayr. Dynamic optimization of metabolic networks coupled with gene expression. In: Journal of Theoretical Biology, 365(0): 469 - 485.

Creators: Henning Lindhorst, Steffen Waldherr

Submitter: Henning Lindhorst

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Originally submitted model file for PLaSMo accession ID PLM_61, version 1

Creators: BioData SynthSys, Martin Beaton

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_22, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn and NAD rec will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn, but no NAD rec, will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with no added Mn, but with NAD rec, will be reproduced.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Steady state model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Originally submitted model file for PLaSMo accession ID PLM_73, version 1

Creators: BioData SynthSys, Yin Hoon Chew

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_76, version 1

Creators: BioData SynthSys, Yin Hoon Chew

Submitter: BioData SynthSys

This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.

The FMv1 links the following sub-models:

  1. Arabidopsis leaf carbohydrate model (Rasse and ...

Creators: Andrew Millar, Yin Hoon Chew

Submitter: Andrew Millar

This ordinary-differential equation model is a spatially lumped model showing the behaviour of oxygen in the three compartments medium, membrane and cytoplasm and its impact on FNR inactivation, hereby showing the effects of different oxygen concentrations, diffusion coefficients and reaction rates. The model was created with the Matlab SimBiology toolbox.

Creator: Samantha Nolan

Submitter: David Knies

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 building:

The module was built using modular bottom-up approach where every module describes a certain process and then, when modules are connected together like domino tiles, we can reconstruct the emergent behavior of the whole system.

This is a blueprint model and might be used for various country/data. If one wans to use it for a particular country/data, we can recommend following steps:

  1. Adjust total population by changing initial condition of A-Initial_population_innocent_non-tested ...

Creators: Alexey Kolodkin, Hans V. Westerhoff

Submitter: Alexey Kolodkin

No description specified

Creator: Vincent Wagner

Submitter: Vincent Wagner

Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material: TNF and MMP7 concentration upgrade of the models All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF ...

Creators: Hans V. Westerhoff, Abulikemu Abudukelimu and Matteo Barberis

Submitter: Hans V. Westerhoff

Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material: TNF and MMP7 concentration upgrade of the models All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF ...

Creators: Hans V. Westerhoff, Ablikim Abulikemu, Matteo Barberis

Submitter: Hans V. Westerhoff

Here is a kinetic model (in COPASI format) of L. lactis glycolysis.

Creator: Mark Musters

Submitter: Mark Musters

Core model with the addition of a NoxE reaction to regenerate NAD using O2. COPASI’s build in Evolutionary programming algorithm was used to estimate parameters using a maximum of 2000 generations with a population size of 100 models with value scaling as weights to train the 5 parameters of the NoxE reaction.

Creator: Niels Zondervan

Submitter: Niels Zondervan

COVID-19 Causal Networks: The SIGNOR team has curated the causal relationships that, according to available evidence, are likely to be relevant for the COVID-19 pathology. The perturbations caused by viral infection are integrated into the cell networks. Evidence obtained using related human coronaviruses diseases such as SARS and MERS are also mapped to the networks. Most of these are indirect relationships as few mechanistic details are clarified to date. As new evidence will be published, it ...

Creators: Luana Licata, Marta Iannuccelli, University of Rome Tor Vergata, IT

Submitter: Marek Ostaszewski

A collection of WikiPathways describing various COVID-19 mechanisms.

Creators: Alexander Pico, Chris Evelo, Rex D A B, Egon Willighagen, Lauren J. Dupuis, Matthew Conroy, Friederike Ehrhart, Kristina Hanspers, Amber Koning

Submitter: Marek Ostaszewski

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