Models
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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
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
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
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
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
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Not specified
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
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
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 type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
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
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Matlab
SBML file supplementary material of the publication.
Creators: Fiona Achcar, Barbara Bakker, Mike Barrett, Rainer Breitling, Eduard Kerkhoven
Submitter: Fiona Achcar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
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
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
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 type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
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
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
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
Model type: Agent based modelling
Model format: Matlab package
Environment: Matlab