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3PG

Format: SimileXMLv3

Contact/Model Admin: robertm

Submission Date: 2010-06-16 14:54:54.0

"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 primary productivity, carbon allocation, and stand growth. The model has the capacity for specifying thinning regimes, although the function needs further refinement. In recent iterations, the 3PG model has been linked to satellite imagery of canopy photosynthetic capacity to model forest growth across landscapes (Coops et al. 1998). Intended as a practical management tool, the model is under constant revision to incorporate new research data, simplify application, and broaden its usefulness. Belowground processes and allocation are one of the least developed aspects of this model and we hope to contribute to the model's development with our envisioned research and application."

http://www.fsl.orst.edu/mycology/ss/3PG.htm

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AFRC Wheat 2 evapw submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:17:42.0

Penman Evaporation over water ( mm/day ). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).

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AFRC Wheat 2 jdaydif submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:24:25.0

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).  

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AFRC Wheat 2 julday submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:30:45.0

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).

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AFRC Wheat 2 ldim submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:40:16.0

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.

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AFRC Wheat 2 photpd submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:46:39.0

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 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.

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AFRC Wheat 2 tdays submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:51:52.0

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 the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box.

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AFRC Wheat 2 vappres submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:55:57.0

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).

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AFRC Wheat 2 vernal submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 16:01:34.0

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.

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AFRC Wheat 2 weathr submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 16:08:23.0

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.

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AFRC Wheat2 dev submodel

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2011-02-04 15:06:59.0

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.

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Arabidopsis - starch and the circadian clock, Model 1 (Seaton et al., 2013)

Format: SBML L2 V4

Contact/Model Admin: dseaton

Submission Date: 2013-11-21 15:25:56.0

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".

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Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 2013)

Format: SBML L2 V4

Contact/Model Admin: dseaton

Submission Date: 2013-11-21 15:28:15.0

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".

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Arabidopsis - starch and the circadian clock, Model 3 (Seaton et al., 2013)

Format: SBML L2 V4

Contact/Model Admin: dseaton

Submission Date: 2013-11-21 15:30:23.0

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".

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Arabidopsis clock model P2011, graphical diagram

Format: SBGN-ML PD

Contact/Model Admin: amillar2

Submission Date: 2015-09-07 21:12:19.0

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 <sbgn> tag was back-edited from the correct string <sbgn xmlns="http://sbgn.org/libsbgn/0.2"> to <sbgn xmlns="http://sbgn.org/libsbgn/pd/0.1"> in this file. The file is still correctly opened in VANTED after this modification. The unmodified version is also attached.

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Arabidopsis clock model P2011.3.1

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2015-09-02 19:11:43.0

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 supercomputer HECTOR, as described in Flis et al. RSOB 2015.

In the model name, Plasmo ID PLM_67 was a private, working version. t30 is the private optimisation run number.

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Arabidopsis clock model P2011.4.1

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2015-09-02 19:14:50.0

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 supercomputer HECTOR, as described in Flis et al. RSOB 2015.

In the model name, Plasmo ID PLM_67 was a private, working version. t34 is the private optimisation run number.

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Arabidopsis clock model P2011.5.1

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2015-09-02 19:17:19.0

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 supercomputer HECTOR, as described in Flis et al. RSOB 2015.

In the model name, Plasmo ID PLM_67 was a private, working version. t37 is the private optimisation run number.

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Arabidopsis clock model P2011.6.1

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2015-09-02 19:18:47.0

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 supercomputer HECTOR, as described in Flis et al. RSOB 2015.

In the model name, Plasmo ID PLM_67 was a private, working version. t40 is the private optimisation run number.

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Arabidopsis clock models P2011.1.2 and P2011.2.1

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2013-06-15 14:08:52.0

The models in this record were 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.

Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6

This model file has two versions, P2011.1.2 and P2011.2.1.

P2011.1.2 is public model ID PLM_71 version 1. Dynamics identical to P2011.1.1 but changes:

  1. updated formulation for light input (now uses ISSF of Adams et al. J Biol Rhythms 2012),
  2. formula for parameters m1 and m2 revised in Copasi, to cL_m degradation to ensure light rate > dark rate. Value of m1 previously 0.54, now 0.3. Simulation in Copasi was identical to earlier version.
  3. Parameter constraints added for SBSI optimisation.
  4. ISSF set to match TiMet RNA data under LD-LL, including LDLL transition event at 314h.

P2011.2.1 is public model ID PLM_71 version 2, with parameters optimised by Andrew Millar using SBSI on server sbsidev1, as described in Flis et al. RSOB 2015.

In the model name, Plasmo ID PLM_67 was a private, working version.

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