# Assays

What is an Assay?### Filters

**14**Assays visible to you, out of a total of

**14**

Validation: Validated against the original running in Excel. Each calculation in the model was individually validated as well. Comments on numerical integration: Euler integration with time steps of 1. In Simile the "time units" were set to "day" and execution was for 364 days as the simulation starts at time 0 (not time 1 as in the Excel model). Comments on running Simile model: Users must specify the temperature controlled growing season themselves. To do this use the following steps which take ...

**Submitter**: BioData SynthSys

**Biological problem addressed**: Gene Regulatory Network

**Investigation:** Davey, Chris

**Study:** Miscanmod - PLM_3

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 ...

**Submitter**: BioData SynthSys

**Biological problem addressed**: Gene Regulatory Network

**Investigation:** Davey, Chris

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

**Biological problem addressed**: Gene Regulatory Network

**Investigation:** Davey, Chris

**Originally submitted to PLaSMo on 2010-12-20 14:54:15**

**Submitter**: BioData SynthSys

**Biological problem addressed**: Gene Regulatory Network

**Investigation:** Davey, Chris

**Study:** AFRCtest2 - PLM_25

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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**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

**Biological problem addressed**: Gene Regulatory Network

**Investigation:** Davey, Chris