Assays

Validation Validated against original code running under GNU FORTRAN 95. Comments on numerical integration No integration needed. Comments on running the (Simile) model The variable "num errors" accumulates the number of times the ribulose bis-phosphate limited photosynthesis rate cannot be calculated. See the documentation dialogue for the Simile variable "jl_electron transport" for details.Additional AttributesOriginal Model: Language: FORTRAN 95 Author:Daniel P. Rasse File name of original ...

The first version of the model corresponds to the one published in Pokhilko et al Mol Syst Biol 2010, which is also presented on the Mol. Syst. Biol. website and was submitted to the Biomodels database. Note: minor errors in published supplementary information are documented in a file attached to version 1; the published SBML files are correct. The second version has some names slightly modified for compatibility with the SBSI platform. Both first and second versions have values of  "dawn" fixed ...

The first version of the model corresponds to the one published in Pokhilko et al Mol Syst Biol 2010, which is also presented on the Mol. Syst. Biol. website and was submitted to the Biomodels database. Note: minor errors in published supplementary information are documented in a file attached to version 1; the published SBML files are correct. The second version has some names slightly modified for compatibility with the SBSI platform. Both first and second versions have values of  "dawn" fixed ...

The first version of the model corresponds to the one published in Pokhilko et al Mol Syst Biol 2010, which is also presented on the Mol. Syst. Biol. website and was submitted to the Biomodels database. Note: minor errors in published supplementary information are documented in a file attached to version 1; the published SBML files are correct. The second version has some names slightly modified for compatibility with the SBSI platform. Both first and second versions have values of  "dawn" fixed ...

Model of the arabidopsis circadian clock obtained from the Bio-PEPA model. The model is based on Alexandra Pokhilko's 2010 deterministic model and includes a scaling factor omega to translate from continuous "concentrations" to discrete amounts. Light function is a smooth function switching between 0 and 1, and is parameterised in order to allow to automate experimentation with different light conditions and photoperiods.Related PublicationsMaria Luisa Guerriero, Alexandra Pokhilko, Aurora Piñas ...

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.Version Comments This is a tidied-up and ...

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.Version Comments The last version, which ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Alexandra's P2011 model with skeleton photoperiod for Graf et al.PNAS 2010.

A Copasi file is attached. Note that another version ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Alexandra's P2011 clock model with:

• skeleton photoperiod for Graf et al. PNAS 2010.

• parameter changes to simulated prr9 ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments This version was modified from version 6 in Copasi by replacement of "light function" to L in all equations. Originally submitted ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments this version is similar to version 5 (but csymbol time is replaced to t), it has a graphical representation in Cell Designer, ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments this version has a graphical representation in Cell Designer. It runs in Cell Designer, Copasi and SBSI, but not run optimization ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Corrected version for SBSI with Kevin Stratford's tanh light function, as in the Locke tanh models. Confirmed will now run and ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Pokhilko Arabidopsis clock model as submitted, SBSI compatible and tanh light function of Kevin Stratford Originally submitted ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Final model as submitted but with time changed to t for compatibilty with SBSI Originally submitted to PLaSMo on 2011-07-16 ...

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.Comments Matlab files are attached to version 1 2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukOriginally submitted to PLaSMo on 2011-07-16 12:31:04

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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

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 ...

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 ...

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 ...

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

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 ...