Models

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

Originally submitted model file for PLaSMo accession ID PLM_23, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

No description specified

Creator: Saptarshi Bej

Submitter: Saptarshi Bej

No description specified

Creator: Saptarshi Bej

Submitter: Markus Wolfien

desktop version of NetLogo model of cellular senescence in dermal layer of skin

Creator: Hannah O'Keefe

Submitter: Hannah O'Keefe

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez1) is the basis kinetic model derived from that published by Teusink et al., 2000 (PMID: 10951190).

Creators: Franco du Preez, David D van Niekerk

Submitter: Franco du Preez

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez2) is an oscillating version of the basis kinetic model (dupreez1) derived from that published by Teusink et al., 2000 (PMID: 10951190).

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez3) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996 (PMID: 8813760).

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez4) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996a (PMID: 8813760) as well as the rapid synchronization following the mixing of two yeast cultures that oscillate 180 degrees out of ...

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez5) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the amplitude bifurcation of oscillating yeast cultures in a CSTR setup reported by Hynne et al., 2001 (PMID: 11744196).

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez6) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in cell free extracts of oscillating yeast cultures reported by Das and Busse, 1991 (PMCID: 1260073).

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez7) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the fluorescence signal of NADH in oscillating yeast cultures reported by Nielsen et al., 1998 (PMID: 17029704).

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

No description specified

Creator: Alexey Kolodkin

Submitter: Alexey Kolodkin

The agent-based model involves the representation of each individual molecule of interest as an autonomous agent that exists within the cellular environment and interacts with other molecules according to the biochemical situation. FLAME environmet has beem used for agent-based development. The FLAME framework is an enabling tool to create agent-based models that can be run on high performance computers (HPCs). Models are created based upon extended finite state machines that include message input ...

Creator: Afsaneh Maleki-Dizaji

Submitter: Afsaneh Maleki-Dizaji

Simplified model file for PLaSMo accession ID PLM_50, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_50, version 1

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Simplified model file for PLaSMo accession ID PLM_50, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_50, version 2

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090003.

[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415

Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski

Submitter: Xiaokang Zhang

This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090001.

[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415

Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski

Submitter: Xiaokang Zhang

This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090002.

[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415

Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski

Submitter: Xiaokang Zhang

First darft of a model including glycolysis and the transcription and translation of the enzymes. See the datafile "Information on the darft transcription/translation model." for information.

Creator: Fiona Achcar

Submitter: Fiona Achcar

Dynamic model of glycolysis, pyruvate metabolism and NoxE. The model is parameterized by selecting the best out of 100 parameter set using Copasi's Genetic algorithm with 1000 itterations and 500 simmulatanious models.

An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum, incorporating the effect of pH upon gene regulation and subsequent end-product levels.

The zip file containes 4 models (in SBML), each representing slightly different experimental conditions.

Creators: Sara Jabbari, Sylvia Haus

Submitter: The JERM Harvester

An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum (Haus et al. BMC Systems Biology 2011, 5:10), incorporating the effect of pH upon gene regulation and subsequent end-product levels. This model describes the first of four experiments in which the pH of the culture was shifted. For this experiment acidogenesis at pH 5.7 was maintained for 137 hours, after which the pH control was stopped, allowing the natural metabolic shift to the ...

Creators: Sara Jabbari, Sylvia Haus

Submitter: Franco du Preez

An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum (Haus et al. BMC Systems Biology 2011, 5:10), incorporating the effect of pH upon gene regulation and subsequent end-product levels. This model describes the last of four experiments in which the pH of the culture was shifted. For this experiment the pH shift was reversed compared to the first three (shift from pH 4.5 to 5.7), with the pH control switched off after 129 hours. ...

Creators: Sara Jabbari, Sylvia Haus

Submitter: Franco du Preez

An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum (Haus et al. BMC Systems Biology 2011, 5:10), incorporating the effect of pH upon gene regulation and subsequent end-product levels. This model describes the second of four experiments in which the pH of the culture was shifted. For this experiment acidogenesis at pH 5.7 was maintained for 137.5 hours, after which the pH control was stopped, allowing the natural metabolic shift to ...

Creators: Sara Jabbari, Sylvia Haus

Submitter: Franco du Preez

An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum (Haus et al. BMC Systems Biology 2011, 5:10), incorporating the effect of pH upon gene regulation and subsequent end-product levels. This model describes the third of four experiments in which the pH of the culture was shifted. For this experiment acidogenesis at pH 5.7 was maintained for 121 hours, after which the pH control was stopped, allowing the natural metabolic shift to the ...

Creators: Sara Jabbari, Sylvia Haus

Submitter: Franco du Preez

Powered by
(v.1.14.2)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH