Models

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394 Models visible to you, out of a total of 633

Originally submitted model file for PLaSMo accession ID PLM_71, version 2

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Simplified model file for PLaSMo accession ID PLM_71, 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_71, version 1

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_1041, version 1

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Simplified model file for PLaSMo accession ID PLM_1041, 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

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

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

This is BIOMD0000000005.

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material: TNF and MMP7 concentration upgrade of the models All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF ...

Creators: Hans V. Westerhoff, Abulikemu Abudukelimu and Matteo Barberis

Submitter: Hans V. Westerhoff

Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material: TNF and MMP7 concentration upgrade of the models All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF ...

Creators: Hans V. Westerhoff, Ablikim Abulikemu, Matteo Barberis

Submitter: Hans V. Westerhoff

This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.

Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. ...

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

Submitter: Hans V. Westerhoff

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.

Model that can be used to obtain the figures of Abudulikemu et al 2018: Abudukelimu, A., Barberis, M., Redegeld, F.A., Sahin, N., and Westerhoff, H.V. (2018). Predictable Irreversible Switching Between Acute and Chronic Inflammation. Front Immunol 9, 1596.

Creators: Hans V. Westerhoff, Ablikim Abudukelimu

Submitter: Hans V. Westerhoff

(Abudulikemu et al 2000 (also 2018) Standard model of acute mode Figure 32.

Creators: Hans V. Westerhoff, Ablikim Abudukelimu

Submitter: Hans V. Westerhoff

Particularly figure 2 of of Abudulikemu et al 2020 in press

Creator: Hans V. Westerhoff

Submitter: Hans V. Westerhoff

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

Creator: Hannah O'Keefe

Submitter: Hannah O'Keefe

Originally submitted model file for PLaSMo accession ID PLM_73, version 1

Creators: Yin Hoon Chew, BioData SynthSys

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_75, version 1

Creators: Yin Hoon Chew, BioData SynthSys

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_74, version 1

Creators: Yin Hoon Chew, BioData SynthSys

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_76, version 1

Creators: Yin Hoon Chew, BioData SynthSys

Submitter: BioData SynthSys

The consensus GEM for Saccharomyces cerevisiae, version 8.3.3, maintained on https://github.com/SysBioChalmers/yeast-GEM.

Creator: Eduard Kerkhoven

Submitter: Eduard Kerkhoven

BPG stability notebook

Creator: Jacky Snoep

Submitter: Jacky Snoep

No description specified

Creator: Alexey Kolodkin

Submitter: Alexey Kolodkin

PGK model for S. solfataricus

Creator: Jacky Snoep

Submitter: Jacky Snoep

A small model representing the core carbon network in each cell. For more detail on the model creation see [1]. The model is written in SBML using the RAM extension for use in deFBA. Compatible python software for simulation can be found at https://tinyurl.com/yy8xu4v7

[1] S. Waldherr, D. A. Oyarzún, A. Bockmayr. Dynamic optimization of metabolic networks coupled with gene expression. In: Journal of Theoretical Biology, 365(0): 469 - 485.

Creators: Henning Lindhorst, Steffen Waldherr

Submitter: Henning Lindhorst

This model was created to showcase all functions of the SBML extension RAM. The model can be unr in deFBA with the python software deFBA-Python. The software is freely available at at https://tinyurl.com/yy8xu4v7

Creator: Henning Lindhorst

Submitter: Henning Lindhorst

A minimal model showing the core of resource allocation models as it can either be invested in enzymatic machinery or single biomass components with the best yield. The model is written in SBML using the RAM extension for use in deFBA. Compatible python software for simulation can be found at https://tinyurl.com/yy8xu4v7

Creator: Henning Lindhorst

Submitter: Henning Lindhorst

This SBML file uses the RAM extension and contains a minimal genome scaled model for Saccharomyces cerevisiae. The model is based of Yeast 6.06 and was published first in A.-M. Reimers Thesis "Understanding metabolic regulation and cellular resource allocation through optimization".

Creators: Henning Lindhorst, Alexandra-M. Reimers

Submitter: Henning Lindhorst

Simplified model file for PLaSMo accession ID PLM_9, 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_9, version 2

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

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