Adams, Richard

SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).

What is PlaSMo? PlaSMo stands for Plant Systems-biology Modelling Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

Our aims

To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost To represent these models in a declarative XML-based format, which is closer to the systems biology standard SBML To evaluate the behaviour ...

This model, derived from Biomodels299, is a variant of the Neurospora Circadian clock model of Leloup et al., 1999. It is supplemented with a periodic light function (SBO:0000475) that is parameterized to produce sinusoidal oscillations in the light sensitive parameter Vs with an amplitude of 5. These sinusoidal wave-form maintains entrained oscillations even with high light input, and is described in Figures 6 and 7 of Gonze and Goldbeter, 2000.Related PublicationsDidier Gonze and Albert Goldbeter ...

 This model is derived from Biomodels 299 - the Leloup et al Neurospora clock model. This variant contains an embedded light-forcing function (SBO:000475) that provides a periodic light input. In this model, after 72h of LD12:12, the amplitude of Vs ( the light dependent parameter ) increases to 4.1, leading to chaotic oscillations. For this to happen, the periodic light function needs to produce a square-wave pattern.    Execution of this model will result in the behaviour depicted in Figure 2D ...

This is a modified version of Biomodels89, containing a light-forcing function. This variant is configured to run cycles of LD8:16Related Publicationsocke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ. (2006). Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. . Mol Syst Biol . Originally submitted to PLaSMo on 2012-03-29 10:24:44

This is a modified version of Biomodels89, containing a light-forcing function. This variant is configured to run cycles of LD8:16Related Publicationsocke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ. (2006). Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. . Mol Syst Biol . Originally submitted to PLaSMo on 2012-03-29 10:24:44

 This model is derived from Biomodels 299 - the Leloup et al Neurospora clock model. This variant contains an embedded light-forcing function (SBO:000475) that provides a periodic light input. In this model, after 72h of LD12:12, the amplitude of Vs ( the light dependent parameter ) increases to 4.1, leading to chaotic oscillations. For this to happen, the periodic light function needs to produce a square-wave pattern.    Execution of this model will result in the behaviour depicted in Figure 2D ...

This model, derived from Biomodels299, is a variant of the Neurospora Circadian clock model of Leloup et al., 1999. It is supplemented with a periodic light function (SBO:0000475) that is parameterized to produce sinusoidal oscillations in the light sensitive parameter Vs with an amplitude of 5. These sinusoidal wave-form maintains entrained oscillations even with high light input, and is described in Figures 6 and 7 of Gonze and Goldbeter, 2000.Related PublicationsDidier Gonze and Albert Goldbeter ...

Data file for PLaSMo accesssion ID PLM_52, version 1

Data file for PLaSMo accesssion ID PLM_52, version 1

Data file for PLaSMo accesssion ID PLM_52, version 1

Data file for PLaSMo accesssion ID PLM_51, version 1

Data file for PLaSMo accesssion ID PLM_51, version 1

Data file for PLaSMo accesssion ID PLM_51, version 1

Data file for PLaSMo accesssion ID PLM_66, version 1

Data file for PLaSMo accesssion ID PLM_51, version 1

Data file for PLaSMo accesssion ID PLM_66, version 1

Data file for PLaSMo accesssion ID PLM_66, version 1

Originally submitted model file for PLaSMo accession ID PLM_52, version 1

Simplified model file for PLaSMo accession ID PLM_52, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_51, version 1

Simplified model file for PLaSMo accession ID PLM_51, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_66, version 1

Simplified model file for PLaSMo accession ID PLM_66, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)