Models

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

To obtain each of the figure 2A - 2E please download "Main Figure Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.

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

Submitter: Alexey Kolodkin

No description specified

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

Submitter: Alexey Kolodkin

No description specified

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

Submitter: Alexey Kolodkin

HSD11B1 inhibition by AZD4017 and the effect on cortisone and 11KA4 metabolism was simulated in Mathematica. Figure 6 of the manuscript is reproduced in the notebook.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Mathematica notebook for simulation of combined effect of HSD11B1/AKR1C3 ratio variation and HSD11B1 inhibition, surface plots are generated shown in Fig. 4 of the manuscript.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Quorum sensing(QS) allows the bacteria to monitor their surroundings and the size of their population. Staphylococcus aureus makes use of QS to regulate the production of virulence factors. This mathematical model of the QS system in S aureus was presented and analyzed (Journal of Mathematical Biology(2010) 61:17–54) in order to clarify the roles of the distinct interactions that make up the QS process, demonstrating which reactions dominate the behaviour of the system at various timepoints. ...

Creators: Sara Jabbari, John King, Adrian Koerber, Paul Williams

Submitter: Franco du Preez

Bacillus subtilis cells may opt to forgo normal cell division and instead form spores if subjected to certain environmental stimuli, for example nutrient deficiency or extreme temperature. The gene regulation net-work governing sporulation initiation accordingly incorporates a variety of signals and is of significant complexity. The present model (Bulletin of Mathematical Biology (2011) 73:181–211) includes four of these signals: nutrient levels, DNA damage, the products of the competence genes, ...

Creators: Sara Jabbari, John Heap, John King

Submitter: Franco du Preez

An ODE model of the gene regulation network governing sporulation initiation in Bacillus subtilis to be run in Matlab.

The network incorporates four sporulation-related signals: nutrient supply, DNA damage, the products of the competence genes and the bacterial population size.

Run execute_bacillus_sporulation_initiation.m to simulate the model. This file also contains the signal-related parameters which can be altered to investigate the effect of competing signals.

Some results for this model ...

Creator: Sara Jabbari

Submitter: Sara Jabbari

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

Originally submitted model file for PLaSMo accession ID PLM_11, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_11, version 2

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Metabolic model of Sulfolobus solfataricus P2 in the SBML (xml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or L-fucose as sole carbon source. Different theoretical routes of L-fucose degradation were modeled (E. coli-like, Xanthomonas-like and lactaldehyde-forming). Highest overall agreement between the model and experimental data was observed for the lactaldehyde-forming route.

Creators: Jacqueline Wolf, Helge Stark, Dietmar Schomburg

Submitter: Jacqueline Wolf

Metabolic model of Sulfolobus solfataricus P2 in the SBML (sbml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or caseinhydrolysate as sole carbon source.

Creator: Helge Stark

Submitter: Helge Stark

Originally submitted model file for PLaSMo accession ID PLM_3, version 1

Creators: BioData SynthSys, Chris Davey

Submitter: BioData SynthSys

The model describes the Entner-Doudoroff pathway in Sulfolobus solfataricus under temperature variation. The package contains source code written in FORTRAN as well as binaries for Mac OSX, Linux, and Windows. If compiling from source code, a FORTRAN compiler is required. On-line versions of the model are also available at: http://bioinfo.ux.uis.no/sulfosys http://jjj.biochem.sun.ac.za/sysmo/projects/Sulfo-Sys/index.html

Creator: Peter Ruoff

Submitter: Peter Ruoff

This mechanistic ODE model describes the growth dynamics of P. aeruginosa, including an antibiotic-induced morphological transition to a fragile spherical form.

Creators: Chloe Spalding, Sara Jabbari

Submitter: Chloe Spalding

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.

Model of reconstituted gluconeogenesis system in S. solfataricus based on the individual kinetic models for PGK, GAPDH, TPI, FBPAase.

Creator: Jacky Snoep

Submitter: Jacky Snoep

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 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

This model assumes a phenotypic switch between an acid- and solvent-forming population caused by the changing pH levels. The two phenotypes differ in their transcriptomic, proteomic, and ,thus, their metabolomic profile. Because the growth rates of these phenotypes depends on the extracellular pH, the initiation of the pH-shift results in a significant decline of the acidogenic population. Simultaneously, the solvent-forming population rises and establishes an new steady state.

The model is build ...

Creators: Thomas Millat, Graeme Thorn, Olaf Wolkenhauer, John King

Submitter: Thomas Millat

SBML file supplementary material of the publication.

Creators: Fiona Achcar, Barbara Bakker, Mike Barrett, Rainer Breitling, Eduard Kerkhoven

Submitter: Fiona Achcar

Fixed parameter model, where the glycolysis model of bloodstream form T. brucei is extended with the pentose phosphate pathway and an ATP:ADP antiporter over the glycosomal membrane. Non-final version.

Creators: Eduard Kerkhoven, Fiona Achcar

Submitter: Eduard Kerkhoven

Fixed parameter model, where the glycolysis model of bloodstream form T. brucei is extended with the pentose phosphate pathway and a ribokinase in the glycosome. Non-final version.

Creators: Eduard Kerkhoven, Fiona Achcar

Submitter: Eduard Kerkhoven

Model of unselective destruction in a single population of cells with differing sensitivities for growth

Creator: James Wordsworth

Submitter: James Wordsworth

Mathematica notebook with model simulation of metabolite profiles after 24h incubation with different ratios of HSD11B1 and AKR1C3 transfected HEK293 cells.

Creator: Jacky Snoep

Submitter: Jacky Snoep

HSD11B1 was inhibited by CBX and the effect on cortisone and 11KA4 conversion was simulated. Model simulated in Mathematica, Figure 3 panels are presented.

Creator: Jacky Snoep

Submitter: Jacky Snoep

No description specified

Creator: Maria Krantz

Submitter: Maria Krantz

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

Simplified model file for PLaSMo accession ID PLM_1010, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Creators: BioData SynthSys, Daniel Seaton

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_1010, version 1

Creators: BioData SynthSys, Daniel Seaton

Submitter: BioData SynthSys

SBML models without activity of the glycolytic enzymes in the cytosol:

Glycolysis_noActivityInCytosol_1a.xml Model 1a Glycolysis_noActivityInCytosol_1b.xml Model 1b Glycolysis_noActivityInCytosol_2.xml Model 2 Glycolysis_noActivityInCytosol_3.xml Model 3 Glycolysis_noActivityInCytosol_4.xml Model 4 Glycolysis_noActivityInCytosol_5.xml Model 5 Glycolysis_noActivityInCytosol_6.xml Model 6

SBML models with activity of the glycolytic enzymes in the cytosol:

Glycolysis_withActivityInCytosol_1a.xm Model ...

Creator: Fiona Achcar

Submitter: Fiona Achcar

Simplified model file for PLaSMo accession ID PLM_66, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Creators: BioData SynthSys, Richard Adams

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_66, version 1

Creators: BioData SynthSys, Richard Adams

Submitter: BioData SynthSys

The zip folder contains files that allow simulation of stressosome dynamics. The models are based on a cellular automaton approach. Each protein of RsbR and RsbS is located in the crystal structure of the stressosome. The proteins can be phosphorylated or not and these states determine the future of neighbouring proteins. To simulate the model open the file 'liebal_stressosome-model_12_workflow-matlab.m' in Matlab. It is written in the cell-model, put the cursor into a cell that you wish to ...

Creator: Ulf Liebal

Submitter: Ulf Liebal

Spatio-temporal liver zonation in mouse and human with Wnt-Hh crosstalk and transport are modeled using coupled partial differential equations. The model file is in MorpheusML format and can be opened in the free, open-source multicellular modeling software Morpheus (https://morpheus.gitlab.io). In Morpheus, the model will simulate the time course (movie) of dynamic liver zonation for a 2D cross-section of several liver lobules, showing the patterns of Wnt ligands, intracellular Wnt signaling, ...

Creators: Lutz Brusch, Jörn Starruß, Michael Kücken

Submitter: Lutz Brusch

The model is adapted from A.P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bökel (2013) Phosphorylation of the Smo tail is controlled by membrane localization and is dispensable for clustering, J. Cell Sci., 126, 20, 4684-4697 doi: 10.1242/​jcs.128926

The model format is MorpheusML that can readily be loaded and run in Morpheus: https://imc.zih.tu-dresden.de//wiki/morpheus

Creator: Lutz Brusch

Submitter: Lutz Brusch

For the spatio-temporal dynamics of bile transport, bile canalicular dilation, mechanical stimulation and transduction of YAP signaling during liver regeneration see the open access publication and its appendix: Meyer et al. (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985. https://doi.org/10.15252/msb.20198985

The model format is MorpheusML that can readily be loaded and run in the free and open source software ...

Creator: Lutz Brusch

Submitter: Lutz Brusch

Morpheus is the modelling and simulation framework for multicellular systems biology developed at Technische Universität Dresden. Manual, examples and binaries for Windows, Linux, MacOS at: https://imc.zih.tu-dresden.de/wiki/morpheus Open source code at: https://gitlab.com/morpheus.lab/morpheus

Creators: Lutz Brusch, Jörn Starruß, Walter de Back, Andreas Deutsch

Submitter: Lutz Brusch

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