Models

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.

Mathematic notebook for enzyme kinetic analysis and model fit, including figure generation for manuscript.

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.

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.

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. ...

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, ...

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 ...

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

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

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.

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.

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

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

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

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.

Unzip model notebooks and keep in the same folder. Notebook "0, generate_model.nb" needs to be run before the others can be, as the model needs to be exported as Excel files before they cvan be used to make the figures.

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

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

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.

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 ...

SBML file supplementary material of the publication.

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.

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.

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

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

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

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. ...

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

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

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 ...

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

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

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 ...

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, ...

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

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 ...

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