Models

Originally submitted model file for PLaSMo accession ID PLM_12, version 1

The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.

The model is described ...

Originally submitted model file for PLaSMo accession ID PLM_33, version 1

Originally submitted model file for PLaSMo accession ID PLM_34, version 1

Originally submitted model file for PLaSMo accession ID PLM_35, version 1

Originally submitted model file for PLaSMo accession ID PLM_36, version 1

Originally submitted model file for PLaSMo accession ID PLM_37, version 1

Originally submitted model file for PLaSMo accession ID PLM_38, version 1

Originally submitted model file for PLaSMo accession ID PLM_39, version 1

Originally submitted model file for PLaSMo accession ID PLM_40, version 1

Originally submitted model file for PLaSMo accession ID PLM_41, version 1

Originally submitted model file for PLaSMo accession ID PLM_32, version 1

The model presents the response of E.coli to different levels of oxygen supply, in which the oxidases, Cyo and Cyd, and their regulators, FNR and ArcBA systems, are included. The initial file 0.xml and supporting documents are for the model with FNR only. Four 0.xml files provided are at AAU level 31, 85, 115 and 217 respectively. The ArcBA system can be activated by revising the number of agents, ArcB, ArcA dimer, ArcA monomer, ArcA tetramer and ArcA octamer, in the initial file. The model needs ...

Mathematica notebook for the parameterisation of the ALD rate equation based on SEEK linked experimental data.

The impact of SARS-CoV-2 on the apoptosis pathway

Simplified model file for PLaSMo accession ID PLM_77, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_77, version 1

A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover", J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2". The other model variants are all available from www.plasmo.ed.ac.uk as stated in the publication. Note that the 'P2011' circadian clock model was modified for this publication (as described), in order to replicate the ...

Simplified model file for PLaSMo accession ID PLM_78, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_78, version 1

Simplified model file for PLaSMo accession ID PLM_79, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_79, version 1

Originally submitted model file for PLaSMo accession ID PLM_1045, version 1

This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.

http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1

Simplified model file for PLaSMo accession ID PLM_71, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_71, version 1

Simplified model file for PLaSMo accession ID PLM_71, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

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

Simplified model file for PLaSMo accession ID PLM_1041, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)