Models

269 Models visible to you, out of a total of 494

Originally submitted model file for PLaSMo accession ID PLM_1, version 1

Creators: BioData SynthSys, Chris Davey

Contributor: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_22, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Contributor: BioData SynthSys

Here is a kinetic model (in COPASI format) of L. lactis glycolysis.

Creator: Mark Musters

Contributor: Mark Musters

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

Contributor: Henning Lindhorst

Originally submitted model file for PLaSMo accession ID PLM_61, version 1

Creators: BioData SynthSys, Martin Beaton

Contributor: BioData SynthSys

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

Creators: BioData SynthSys, Yin Hoon Chew

Contributor: BioData SynthSys

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

Creators: BioData SynthSys, Yin Hoon Chew

Contributor: BioData SynthSys

This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.

The FMv1 links the following sub-models:
1. Arabidopsis leaf carbohydrate model (Rasse and
...

Creators: Andrew Millar, Yin Hoon Chew

Contributor: Andrew Millar

This ordinary-differential equation model is a spatially lumped model showing the behaviour of oxygen in the three compartments medium, membrane and cytoplasm and its impact on FNR inactivation, hereby showing the effects of different oxygen concentrations, diffusion coefficients and reaction rates. The model was created with the Matlab SimBiology toolbox.

Creator: Samantha Nolan

Contributor: David Knies

Core model with the addition of a NoxE reaction to regenerate NAD using O2. COPASI’s build in Evolutionary programming algorithm was used to estimate parameters using a maximum of 2000 generations with a population size of 100 models with value scaling as weights to train the 5 parameters of the NoxE reaction.

Creator: Niels Zondervan

Contributor: Niels Zondervan

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