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Millar lab working model, extends the Arabidopsis clock model by incorporating multiple sites of inhibition of clock gene expression by TOC1. Model is included into submitted publication "Global Mapping at the Core of the Arabidopsis Circadian Clock Defines a Novel Network Structure of the Oscillator" with Paloma Mas Version 1 has two errors corrected in version 2. This private record is now superseded by the published version, which is public as PLM_70.Originally submitted to PLaSMo on 2011-12-29 ...
Submitter: BioData SynthSys
Investigation: Pokhilko, Alexandra
Assays: Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 1, Arabidopsis_clock_2012_TOC1_repressor - PLM_49, version 2
Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.
Originally submitted to PLaSMo on 2011-07-16 12:31:04
Submitter: BioData SynthSys
Investigation: Pokhilko, Alexandra
Assays: Arabidopsis_clock_2011 - PLM_43, version 1, Arabidopsis_clock_2011 - PLM_43, version 2, Arabidopsis_clock_2011 - PLM_43, version 3, Arabidopsis_clock_2011 - PLM_43, version 4, Arabidopsis_clock_2011 - PLM_43, version 5, Arabidopsis_clock_2011 - PLM_43, version 6, Arabidopsis_clock_2011 - PLM_43, version 7, Arabidopsis_clock_2011 - PLM_43, version 8, Arabidopsis_clock_2011 - PLM_43, version 9
Validation. Validated against original implementation running under GNU FORTRAN 95. To allow the maximum flexiblity during validation the original FORTRAN code was modified slightly (note that no code lines were deleted). The code was run with high precision so that values were directly comparable with those in Simile even after hundreds of thousands of iterations. The values of all the variables in the original code were printed to the screen so that they could be checked against their Simile ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
Assays: Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - PLM_2, 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 3".Related PublicationsSeaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental approaches to the circadian control of starch turnover. Journal of the Royal Society Interface. Originally submitted ...
Submitter: BioData SynthSys
Investigation: Seaton, Daniel
Assays: Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 20...
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".Related PublicationsSeaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental approaches to the circadian control of starch turnover. Journal of the Royal Society Interface. Originally submitted ...
Submitter: BioData SynthSys
Investigation: Seaton, Daniel
Assays: Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 20...
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 1".Related PublicationsSeaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental approaches to the circadian control of starch turnover. Journal of the Royal Society Interface. Originally submitted ...
Submitter: BioData SynthSys
Investigation: Seaton, Daniel
Assays: Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 20...
Originally submitted to PLaSMo on 2010-12-20 14:54:15
To calculate the phenological stage of the crop. Note the following definition: phase = the period between two phenological stages, ie. the phase sowing to emergence. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box. Euler integration with 1 day time steps.Related ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). Reads and processes todays weather data. Calculates Penman evaporation and converts day/month/year to Julian day (allowing for year change and leap years). We acknowledge Mikhail Semenov for kindly allowing us to supply this Rothamsted weather data set with this model. Euler integration with 1 day time steps.Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
To return today's vernalising effect (see Weir,A.H. et al.,(1984).J.Agric.Sci.,Camb.,102,371-382). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box.Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
To return Vapour pressure calculated from Wet and Dry Bulb Temperatures. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).
Related Publications
Porter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen.. Eur. J. Agron. 2(2): 69-82..
Originally submitted to PLaSMo on 2011-02-04 15:55:57
Submitter: BioData SynthSys
Investigation: Davey, Chris
To return daily thermal time with base TBASE. Thermal time for a day is calculated by splitting the 24 hour period into 8 * 3 hour periods whose relative contribution to thermal time for the day is based on a cosinusoidal variation in temperature between observed maximum and minimum values. See Weir,A.H. et al.,(1984).J.Agric.Sci.,Camb.,102,371-382. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
To calculate today's daylength and photoperiod. Daylength is calculated following the treatment of Sellers, Physical Climatology,pp 15-16 and Appendix 2. Daylength is calculated with a correction for atmospheric refraction equivalent to 50 minutes of a degree. Photoperiod is calculated assuming that light is perceived until the centre of the sun is 6 degrees below the horizon. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
To calculate leaf and sheath dimensions for main stems and tillers given the emergence length of their leaves and empirical relationships linking leaf number to maximum laminar length. All sizes are in mm. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box.Related ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
Transform Calendar day to Julian Day. Converts day, month, year into the equivalent Julian Day allowing for leap years. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82.. Originally submitted to PLaSMo on 2011-02-04 15:30:45
Submitter: BioData SynthSys
Investigation: Davey, Chris
Number of days between 2 Julian days allowing for change of year and leap years. Assumptions : The gap between the two dates is less than 1 year also JDAY1 is before JDAY2. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82.. Originally submitted to PLaSMo on 2011-02-04 15:24:25 ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
Penman Evaporation over water ( mm/day ). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).
Related Publications
Porter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82..
Originally submitted to PLaSMo on 2011-02-04 15:17:42
Submitter: BioData SynthSys
Investigation: Davey, Chris
"3PG is an acronym for Physiological Principles Predicting Growth. It is a generalized forest carbon allocation model, published by Landsberg and Waring (1997), that works with any forest biome and can be run as an Excel spreadsheet by practicing foresters given a few days of training. The model uses relatively simple and readily available inputs such as species growth tables, latitude, aspect, weather records, edaphic variables, stand age, and stand density to derive monthly estimates of gross ...
To investigate amino acid degradation pathways in Sulfolobus solfataricus transcriptome, proteome and metabolome analyses were performed on cells grown on caseinhydrolysate as carbon source. Cells grown with glucose served as reference condition. Metabolic modelling was used to compare the efficiency of different degradation routes.
Submitter: Jacqueline Wolf
Investigation: Amino acid degradation in Sulfolobus solfataric...
Assays: Metabolic modelling of S. solfataricus during growth on casaminoacids, Metabolome analysis: Casaminoacids versus D-Glc, Proteome analysis: Casaminoacids versus D-Glc, RNA sequencing: Casaminoacids vs D-glc
Altering the light:dark cycle of standard growth conditions and standard 'wild-type' Arabidopsis accession, with sucrose, starch and biomass data for whole rosettes
Submitter: Andrew Millar
Investigation: Arabidopsis Framework Model v1, predicting rose...
Standard growth conditions and standard 'wild-type' Arabidopsis accession, with biomass data for whole rosettes, and in some cases, individual leaf area and leaf biomass data
Submitter: Andrew Millar
Investigation: Arabidopsis Framework Model v1, predicting rose...
Assays: Growth of Col-0 in 12hL:12hD
Standard growth conditions and 'wild-type' Arabidopsis accessions other than Col-0 and the 35S:miR156 transgenics, with biomass data for whole rosettes, and in some cases, individual leaf area and leaf biomass data
The FMv1 was constructed from 4 existing models, with Matlab and Simile versions.
Submitter: Andrew Millar
Investigation: Arabidopsis Framework Model v1, predicting rose...
Assays: Arabidopsis Framework Model v1, Matlab and Simile version
D Biphasic control of stem-cell expansion, where stem-cell expansion is low both at high and low concentrations of y. The system has a stable fixed point at the concentration of y where pr = 0.5 and an unstable fixed point at some lower concentration of y.
SED-ML simulation https://jjj.bio.vu.nl/models/experiments/karin2017_fig4d/simulate
Submitter: Jacky Snoep
Investigation: Karin et al (2017) Molecular Systems Biology
Assays: Biphasic control can provide mutant resistance to stem-cell homeostatic ...
C A mutated stem cell with a strong inactivation of the sensing of y has a growth advantage (differentiates less), and therefore, it invades the stem- cell population. As a result, both the stem-cell pool and the number of terminally differentiated cells increase.
SED-ML simulation https://jjj.bio.vu.nl/models/experiments/karin2017_fig4c/simulate
Submitter: Jacky Snoep
Investigation: Karin et al (2017) Molecular Systems Biology
Assays: Biphasic control can provide mutant resistance to stem-cell homeostatic ...
Mathematical simulation of a tamoxifen-induced conditional knock-in of a sixfold activating GCK mutant in beta cells. (C) The percentage of beta cells with mutated GCK increases to ~25% after 3 days, but then decreases and is eliminated after a few weeks. (D) Glucose levels initially decrease after the tamoxifen injection, but return to normal after a few weeks. Insets: Experimental results of Tornovsky-Babeay et al (2014).
SED-ML simulation https://jjj.bio.vu.nl/models/experiments/karin2017_fig2/simulate ...
Submitter: Jacky Snoep
Investigation: Karin et al (2017) Molecular Systems Biology
Assays: Frequency-dependent selection of mutant pancreatic beta cells.
C Trajectories of Z from different initial concentrations of cells (Z) (i) or y (ii) for the circuit of (B). The healthy concentration Z = ZST is reached regardless of initial concentration of Z, as long as it is nonzero, and regardless of the initial concentration of y.
SED-ML simulation https://jjj.bio.vu.nl/models/experiments/karin2017_fig1c/simulate
Submitter: Jacky Snoep
Investigation: Karin et al (2017) Molecular Systems Biology
Assays: Biphasic control can resist mutant invasion of feedback circuits.
D An arrow marks the time when a mutant with a strong activation of the sensing of y arises (for the circuit depicted in B). This mutant has a selective advantage and takes over the population.
SED-ML simulation https://jjj.bio.vu.nl/models/experiments/karin2017_fig1d/simulate
Submitter: Jacky Snoep
Investigation: Karin et al (2017) Molecular Systems Biology
Assays: Biphasic control can resist mutant invasion of feedback circuits.
G Trajectories of Z from different initial concentrations of Z (i) or y (ii) for the circuit depicted in (F). The healthy concentration Z = ZST is not reached for small values of Z (Z << ZST) or large values of y (y >> yUST).
SED-ML simulation https://jjj.bio.vu.nl/models/experiments/karin2017_fig1g/simulate
Submitter: Jacky Snoep
Investigation: Karin et al (2017) Molecular Systems Biology
Assays: Biphasic control can resist mutant invasion of feedback circuits.