Troein, Carl

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 is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).

Originally submitted to PLaSMo on 2010-05-04 11:27:33

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by setting its value to 1. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally submitted to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by replacing it with immediate light input. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by replacing it with immediate light input. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by setting its value to 1. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally submitted to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses ...

This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).Comments Not formulated to easily allow addition of the ISSF to replace the present light ...

This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).Comments Not formulated to easily allow addition of the ISSF to replace the present light ...

Data file for PLaSMo accesssion ID PLM_7, version 2

Data file for PLaSMo accesssion ID PLM_89, version 2

Data file for PLaSMo accesssion ID PLM_89, version 1

Data file for PLaSMo accesssion ID PLM_91, version 1

Data file for PLaSMo accesssion ID PLM_90, version 1

Data file for PLaSMo accesssion ID PLM_87, version 1

Data file for PLaSMo accesssion ID PLM_92, version 1

Data file for PLaSMo accesssion ID PLM_85, version 1

Data file for PLaSMo accesssion ID PLM_88, version 1

Data file for PLaSMo accesssion ID PLM_86, version 1

Data file for PLaSMo accesssion ID PLM_83, version 1

Data file for PLaSMo accesssion ID PLM_84, version 1

Simplified model file for PLaSMo accession ID PLM_7, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Simplified model file for PLaSMo accession ID PLM_7, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_7, version 2

Originally submitted model file for PLaSMo accession ID PLM_7, version 1

Originally submitted model file for PLaSMo accession ID PLM_89, version 2

Simplified model file for PLaSMo accession ID PLM_89, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Simplified model file for PLaSMo accession ID PLM_89, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Simplified model file for PLaSMo accession ID PLM_90, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_89, version 1

Simplified model file for PLaSMo accession ID PLM_91, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_90, version 1

Simplified model file for PLaSMo accession ID PLM_92, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_91, version 1

Originally submitted model file for PLaSMo accession ID PLM_92, version 1

Originally submitted model file for PLaSMo accession ID PLM_87, version 1

Simplified model file for PLaSMo accession ID PLM_87, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_88, version 1

Simplified model file for PLaSMo accession ID PLM_88, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_85, version 1

Simplified model file for PLaSMo accession ID PLM_85, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)