Models
What is a Model?Filters
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
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
Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.
Creator: Andrew Millar
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
The P2011.3.1 SBML model imported into Copasi v4.8, saved as native Copasi file
Creators: Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Arabidopsis clock model P2011.6.1 SBML imported into Copasi 4.8 and saved as native Copasi file.
Creators: Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC
Submitter: Andrew Millar
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
A diagram encoding PAMP signaling relevant to COVID-19/SARS-CoV-2
Creator: Matti Hoch
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The fitted function describes the pH-drop during 'forward'-shift experiments and the increase of the pH during 'reverse'-shift experiments. The estimated parameters are used to compute the changing pH level in the models of the pH.induced metabolic shift in continuous cultures under phosphate limitation of C. acetobutylicum. Furthermore, the parameters can be applied to join different independent experiments into a single data set.
To fit the changing pH level, an exponential function and a ...
Creator: Thomas Millat
Submitter: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
3D structure prediction of LDH enzymes from four LAB by comparative modeling against x-ray structure of LDH from B. stearothermophilis (template, PDB ID: 1LDN). The computation was performed with a protocol that uses "automodel.very_fast" settings of Modeller program (http://salilab.org/modeller/).
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
Computation is performed for the modeled 3D structures of LDH enzymes (in PDB format) with the UHBD program, for pH 6 and pH 7.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
Comparison of electrostatic potentials within the allosteric binding sites of LDH enzymes to estimate the binding affinity of the FBP molecule is performed with the PIPSA program. The program uses the structure of enzymes in the PDB format and computed electrostatic potentials in the GRD format.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
Binding energies of phosphate ions to the allosteric and catalytic sites were estimated with a program GRID (http://www.moldiscovery.com/soft_grid.php). The calculations were performed for the modeled LDH structures from four LABs, at pH 6 and 7, in presence and absence of the FBP molecule. The phosphate ion was presented as a probe.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Not specified
Model format: Not specified
Environment: Not specified
In order to estimate whether Pi has an activatory or an inhibitory effect on the enzymes, the computed probe binding energies (from GRID results, Part 4) were compared with those for the LDH from L. plantarum whose activity is known to be unaffected by Pi.
The binding energies of the Pi probe in the allosteric binding site (AS) and the COO probe in the catalytic binding site (CS) of LDH from L. plantarum were defined as E¬AS,threshold and ECS,threshold, respectively. For the other LDH enzymes, ...
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
Model type: Algebraic equations
Model format: Not specified
Environment: Not specified
Originally submitted model file for PLaSMo accession ID PLM_75, version 1
Creators: BioData SynthSys, Yin Hoon Chew
Submitter: BioData SynthSys
Model type: Not specified
Model format: Simile XML v3
Environment: Not specified
This partial-differential equations model focuses on the oxygen gradients in consideration of the three-dimensional cell and environment.
Creator: Samantha Nolan
Submitter: David Knies
Model type: Partial differential equations (PDE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the PFK rate equation based on SEEK linked experimental data.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the PGI rate equation based on SEEK linked experimental data.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
PGK model for S. solfataricus
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
PGK 70C SBML
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Mathematical model for PGK kinetics, ADP, ATP, 3PG and BPG saturation.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the PGK rate equation based on SEEK linked experimental data.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
PGK yeast Fig1a
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK yeast with/without recycling
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH model Sulfolobus kouril8
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH model yeast kouril7
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Mathematica notebook for the parameterisation of the PGM rate equation based on SEEK linked experimental data.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Here, we use hyperbolic tangents to fit experimental data of AB fermentation in C. acetobutylicum in continous culture at steady state for different external pHs. The estimated parameters are used to define acidogenic and solventogenic phase. Furthermore, an transition phase is identified which cannot be assigned to acidogenesis or solventogenesis.
Several plots compare the fits to the experimental data.
Creator: Thomas Millat
Submitter: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Mathematica notebook for the parameterisation of the PK rate equation based on the experimental SEEK data set
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Creator: Paul Heusden
Submitter: The JERM Harvester
Model type: Not specified
Model format: Not specified
Environment: Not specified
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with sequential addition of purified enzymes.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.
Creators: Jennifer Levering, Mark Musters
Submitter: Jennifer Levering
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.
Creator: Jennifer Levering
Submitter: Jennifer Levering
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Structural models of the LAB PYKs of L. lactis, L. plantarum, S. pyogenes and E. faecalis including the "best" docking solutions of potential allosteric ligands. The structures were derived by homology modeling based on the template of E. coli and B. stearothermophilus. PYK models and ligands are provided as .pdb files and can be displayed by using the program PyMOL, for instance.
Creators: Nadine Veith, Anna Feldman-Salit, Stefan Henrich, Rebecca Wade
Submitter: Nadine Veith
Model type: Not specified
Model format: Not specified
Environment: Not specified
Pyrimidine deprivation and immune response related to human coronavirus infection
Creators: Zsolt Bocskei, Franck Augé, Anna Niarakis
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Mathematica notebook for the pyruvate transport rate equation, based on literature data.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified