Models
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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
The Folder contains:
- The MCMC and simulation results, as well as the synthetic data of the Chemical Reaction Network model (DoubleDecayIndep)
- The MCMC and simulation results, as well as the synthetic data of the Lotka-Volterra model (LotkaVolterraJoint)
Together with an executable ipynb script (Exe.ipynb) and the MCMC plotting and execution functions (MCMCFunctions.py).
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Creator: Jana Musilova
Submitter: Jana Musilova
Model type: Metabolic network
Model format: Not specified
Environment: Not specified
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
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
Model of selective destruction in a single population of cells with differing sensitivities for growth. Fast growing cells can be epigenetically converted to slower cells rather than simple cell death as in previous models.
Creator: James Wordsworth
Submitter: James Wordsworth
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
Model of unselective destruction in a single population of cells with differing sensitivities for growth
Creator: James Wordsworth
Submitter: James Wordsworth
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
Model of selective destruction in a single population of cells with differing sensitivities for growth
Creators: James Wordsworth, Daryl Shanley, Hannah O'Keefe
Submitter: James Wordsworth
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Not specified
Model format: Not specified
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_1030, version 1
Creators: BioData SynthSys, Uriel Urquiza Garcia, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Model derived from U2019.2, fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the product of scaling factor and either transcription or translation, the latter required for ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Model derived from U2019.1 in which the transcription rates were rescaled to match the scale of TiMet data set for absolute units of RNA concentration. The gmX scaling parameters in the model were fitted numerically. This model has equivalent dynamics to P2011.1.2.
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Model derived from U2020.2, fitted to the TiMet RNA data for wild-type and clock mutants. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rates were obtained by taking the product of scaling factor and either transcription or translation, the ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Model derived from U2020.1 by fitting the scaling factors for matching TiMet data set for wild-type and clock mutants, in absolute units.
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Model derived from U2019.1, in which the way the PRR genes are regulated is modified. Repression mechanism introduced Instead of activation between the PRRs for producing the wave of expression. This is inspired in the result of three models P2012, F2014 and F2016. P2012 introduced TOC1 repression in earlier genes relative to its expression. F2014 introduced also the backward repression of PRR9 |-- PRR7 |--- PRR5, TOC1. However little attention was given to why there is a sharper expression ...
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Model written in Antimony human-readable language and then translate into SBML using Tellurium
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Model written in Antimony human-readable language, Model used in Pokhilko et al 2012
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
autogenerated equation listing from the SBML of U2020.3, as a .PDF file
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: PDF (Model description)
Environment: Not specified
autogenerated equation listing from the SBML of U2019.3, as a .PDF file
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: PDF (Model description)
Environment: Not specified
NLRP3 inflammasome activation
Creators: Julia Somers, Gökçe Yağmur Summak, Ebru Kocakaya
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Thrombotic complications and coagulopathy in COVID-19
Creators: Goar Frischmann, Gisela Fobo, Corinna Montrone
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Kynurenine synthesis pathway
Creators: Julia Somers, Gökçe Yağmur Summak, Ebru Kocakaya
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
TGF beta signalling
Creator: Francesco Messina
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The role of the interaction between the SARS-CoV-2 Spike protein and the renin-angiotensin pathway, in particular human ACE2 in pulmonary blood pressure regulation
Creators: Enrico Glaab, Andreas Ruepp, Corinna Montrone, Gisela Fobo
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The Interferon-lambda (IFNL) map describes the action of the drug candidate IFNL on intra- and intercellular signal transduction under SARS-CoV-2.
Creators: Marius Rameil, Vanessa Nakonecnij, Marta Conti
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The relation of the interferon 2 pathway and SARS-CoV-2.
Creators: Anna Niarakis, Vidisha Singh, Sara Sadat AGHAMIRI
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified