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This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.6.1 is public model ID PLM_1044, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Arabidopsis clock model P2011.6.1 - PLM_1044, version 1
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.5.1 is public model ID PLM_1043, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Arabidopsis clock model P2011.5.1 - PLM_1043, version 1
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.4.1 is public model ID PLM_1042, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Arabidopsis clock model P2011.4.1 - PLM_1042, version 1
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.3.1 is public model ID PLM_1041, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Arabidopsis clock model P2011.3.1 - PLM_1041, version 1
Creator - Dr. Daniel D. Seaton. Graphical overview of Arabidopsis clock model P2011 in SBGN, from SBGN-ED in VANTED v2. N.B. to pass PlaSMo validation before update, the
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Arabidopsis clock model P2011, graphical diagram - PLM_1045, version 1
To check if all works fine after struts update. Checking editorial options
Additional Attributes
tested:
Yes, against schema
Originally submitted to PLaSMo on 2013-11-22 15:15:40
Submitter: BioData SynthSys
Investigation: Zielinski, Tomasz
dfds
Originally submitted to PLaSMo on 2015-09-02 18:27:55
Submitter: BioData SynthSys
Investigation: Zielinski, Tomasz
Construction of a Genome scale constrained-based metabolic modeling of M. hyopneumonia
Submitter: Niels Zondervan
Investigation: Modelling of M. pneumoniae metabolism
Assays: Construction of a Genome Scale Metabolitic model of M. hyopneumoniae
Proteomics Average and SD data for time series data, 6h, 12h, 24h, 48h,72, 96h per protein
Submitter: Niels Zondervan
Investigation: Modelling of M. pneumoniae metabolism
Assays: Proteomics assay
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
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: Troein Ostreococcus clock 1-loop - PLM_7, version 1, Troein Ostreococcus clock 1-loop - PLM_7, version 2
"TRIFFID (Top-down Representation of Interactive Foliage and Flora Including Dynamics)" is a dynamic global vegetation model, which updates the plant distribution and soil carbon based on climate-sensitive CO2 fluxes at the land-atmosphere interface. The surface CO2 fluxes associated with photosynthesis and plant respiration are calculated in the MOSES 2 tiled land-surface scheme (Essery et al (In preparation)), on each atmospheric model timestep (normally 30 minutes), for each of 5 plant functional ...
Cytoscape silqueue specific protein detection
Originally submitted to PLaSMo on 2012-03-02 12:44:13
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 silqueue specific protein detection network - PLM_59, version 1
Cytoscape shoot specific diurnal transcript oscillation.
Originally submitted to PLaSMo on 2012-03-02 12:42:30
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_5...
The seed network, uploaded as a test from Cytoscape
Originally submitted to PLaSMo on 2012-02-24 11:41:50
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 seed network - PLM_53, version 1, TiMet 2011 seed network - PLM_53, version 2
Test for root network
Originally submitted to PLaSMo on 2012-02-27 14:24:59
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
PP interaction network exported from Cytoscape in XGMML
Originally submitted to PLaSMo on 2012-03-02 12:32:33
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 PP interaction network - PLM_56, version 1
Trial upload of the pollen netwrok from TiMet
Originally submitted to PLaSMo on 2012-02-27 12:17:46
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 Pollen network - PLM_54, version 1, TiMet 2011 Pollen network - PLM_54, version 2
TiMet flower specific protein detection network
Originally submitted to PLaSMo on 2012-03-02 12:39:54
Submitter: BioData SynthSys
Investigation: Graf, Alexandra
Assays: TiMet 2011 flower specific protein detection network - PLM_57, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 1, T2011 Ostreococcus clock, TOC1 degr L - PLM_89, version 2
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 degr D - PLM_90, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 act L - PLM_91, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, TOC1 act D - PLM_92, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 prod L - PLM_87, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 prod D - PLM_88, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 degr L - PLM_85, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, CCA1 degr D - PLM_86, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, acc on - PLM_84, version 1
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 ...
Submitter: BioData SynthSys
Investigation: Troein, Carl
Assays: T2011 Ostreococcus clock, acc immediate - PLM_83, version 1
The model is applied to spring wheat, with ample supply of nutrients and water, also without pests, diseases and weeds. Radiation and temperature, being the most important environmental factors, and crop characteristics determine growth and development. Crop growth and development are simulated based on underlying chemical, physiological and physical processes. Dry matter accumulation is calculated from daily crop CO2 assimilation based on leaf CO2 assimilation and taking into account the respiration ...