Models

What is a Model?
161 Models visible to you, out of a total of 252

Parameters rescaled and scaling factors set to 1

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

This is the scaled version of U2020.4 in sbml file. It already contains the scaling factors

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Paramters rescaled and scaling factors set to 1

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Paramteres rescaled and scaling factors set to 1

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Parameters rescaled and scaling factors set to 1

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

Sbml version of U2019.4 with reacaling factors values already incoporated in the model. This was generated autmatically using tellurium python package

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

This file was derived from U2020.3 by introducing the scalig factors in the required locations in the model. This files is used then for numerically rescaling the model for matching synthetic protein data.

Creator: Uriel Urquiza Garcia

Submitter: Uriel Urquiza Garcia

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 ...

Creators: Andrew Millar, Daniel Seaton

Submitter: Andrew Millar

Matlab model (could not be represented in SBML) from publication with abstract: Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription. ...

Creators: Andrew Millar, Daniel Seaton

Submitter: Andrew Millar

Originally submitted model file for PLaSMo accession ID PLM_1030, version 1

Model derived from U2019.2, fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the product of scaling factor and either transcription or translation, the latter required for ...

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2019.1 in which the transcription rates were rescaled to match the scale of TiMet data set for absolute units of RNA concentration. The gmX scaling parameters in the model were fitted numerically. This model has equivalent dynamics to P2011.1.2.

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2020.2, fitted to the TiMet RNA data for wild-type and clock mutants. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rates were obtained by taking the product of scaling factor and either transcription or translation, the ...

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2020.1 by fitting the scaling factors for matching TiMet data set for wild-type and clock mutants, in absolute units.

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2019.1, in which the way the PRR genes are regulated is modified. Repression mechanism introduced Instead of activation between the PRRs for producing the wave of expression. This is inspired in the result of three models P2012, F2014 and F2016. P2012 introduced TOC1 repression in earlier genes relative to its expression. F2014 introduced also the backward repression of PRR9 |-- PRR7 |--- PRR5, TOC1. However little attention was given to why there is a sharper expression ...

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

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 written in Antimony human-readable language, Model used in Pokhilko et al 2012

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

autogenerated equation listing from the SBML of U2020.3, as a .PDF file

Creators: Andrew Millar, Uriel Urquiza Garcia

Submitter: Andrew Millar

autogenerated equation listing from the SBML of U2019.3, as a .PDF file

Creators: Andrew Millar, Uriel Urquiza Garcia

Submitter: Andrew Millar

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.3 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2020.2 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.1 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.3 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

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