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"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
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Penman Evaporation over water ( mm/day ). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).<br><br><strong>Related Publications</strong></strong><br>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.. <br><br><strong>Originally submitted to PLaSMo on 2011-02-04 15:17:42</strong></strong>
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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). &nbsp;<br><br><strong>Related Publications</strong></strong><br>Porter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. .
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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).<br><br><strong>Related Publications</strong></strong><br>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.. <br><br><strong>Originally
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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
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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
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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). &nbsp; &nbsp; All variables and parameters
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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).<br><br><strong>Related Publications</strong></strong><br>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.. <br><br><strong>Originally submitted to PLaSMo on 2011-02-04
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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.<br><br><strong>Related Publications</strong></strong><br>Porter
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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.<br><br><strong>Related Publications</strong></strong><br>Porter
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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
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<br><br><strong>Originally submitted to PLaSMo on 2010-12-20 14:54:15</strong></strong>

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A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko,&nbsp;"Regulatory principles and experimental approaches to the circadian control of starch turnover", &nbsp;J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 1".<br><br><strong>Related Publications</strong></strong><br>Seaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental
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A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko,&nbsp;"Regulatory principles and experimental approaches to the circadian control of starch turnover", &nbsp;J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2".<br><br><strong>Related Publications</strong></strong><br>Seaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental
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A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko,&nbsp;"Regulatory principles and experimental approaches to the circadian control of starch turnover", &nbsp;J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 3".<br><br><strong>Related Publications</strong></strong><br>Seaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental
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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 &lt;sbgn&gt; tag was back-edited from the correct string &lt;sbgn xmlns="http://sbgn.org/libsbgn/0.2"&gt; to &lt;sbgn xmlns="http://sbgn.org/libsbgn/pd/0.1"&gt; in this file. The file is still correctly opened in VANTED after this modification. The unmodified version is also attached.
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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. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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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. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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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. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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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. <strong>Derived from Original model</strong>: P2011.1.2 is public model ID PLM_71 version 1, <a href="http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1">http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&amp;version=1
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The models in this record were published in Flis et al. Royal Society Open Biology 2015. Their original IDs in the PlaSMo resource and IDs in Biomodels are given below. Please select files for download from the 'Related Items' list or the object tree/graph, below. 'SUBMITTED' is the original model version; 'SIMPLIFIED' removes SBML elements that were incompatible with SloppyCell software.

<strong>Original model</strong>: Arabidopsis clock model P2011.1.1 from
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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
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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 <a href="http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64">PLM_64 here</a>.<br><br><strong>Originally submitted to PLaSMo on 2011-07-16 12:31:04</strong></strong>

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.<br><br><strong>Originally
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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.<br><br><strong>Related
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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 <a href="http://www.sbsi.ed.ac.uk">the&nbsp;SBSI
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This model is termed P2011 and derives from the article: <strong>The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops</strong><strong>. </strong>Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday &amp; Andrew J Millar <em>Mol. Syst. Biol. </em>2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. <a href="http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html">Link</a>
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This model is termed P2012 and derives from the article: <strong>Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs</strong>. Alexandra Pokhilko, Paloma Mas &amp; Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. <a href="http://dx.doi.org10.1186/1752-0509-7-23">Link</a> The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It
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P2011 model from PLM_43 version 6, optimised by Andrew Millar with SBSI PGA optimisation. A limited parameter set were free to optimise over &lt; 10-fold range (less for RNA degradation rates), against ROBuST RNA data for clock genes in WT and mutants at 17C in LD, and period data in the same mutants in LL. The full SBSI costing is included, using costs from mid-June 2012 (note that costs returned with original optimisation in May were incorrectly reported).<br><br><strong>Originally
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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.<br><br><strong>Originally submitted to PLaSMo on 2012-05-31 22:18:27</strong></strong>

A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
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A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
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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.<br><br><strong>Additional Attributes</strong></strong><br>Original
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This is the representation of major parts of the central metabolism in monocotyledon plants. The information has been derived from the <a href="http://metacrop.ipk-gatersleben.de/">MetaCrop</a> <a href="http://sourceforge.net/apps/mediawiki/libsbgn/index.php?title=SBGN-ML_Example_Files#2">[2]</a> database, a manually curated repository of high quality information concerning the metabolism of crop plants. This includes pathways, reactions, locations,
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<em>"The CENTURY model is a general model of plant-soil nutrient cycling which is being used to simulate carbon and nutrient dynamics for different types of ecosystems including grasslands, agricultural lands, forests and savannas. &nbsp;CENTURY is composed of a soil organic matter/ decomposition submodel, a water budget model, a grassland/crop submodel, a forest production submodel, and management and events scheduling functions. It computes the flow of carbon, nitrogen, phosphorus,
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dfds <br><br><strong>Originally submitted to PLaSMo on 2015-09-02 18:27:55</strong></strong>

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This is a photothermal model for Arabidopsis that predicts flowering time, published in Chew et al (2012). It is an improved version of the model in Wilczek et al (Science 2009). A Simile version of the model is attached. <strong>Instructions to run the Photothermal Model in Simile</strong> 1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Download the Simile file attached or import the XML into Simile: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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This is the Framework Model (Chew et al, PNAS 2014;&nbsp;<a href="http://www.pnas.org/content/early/2014/08/27/1410238111">http://www.pnas.org/content/early/2014/08/27/1410238111</a>)&nbsp;that links the following: 1. Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - Carbon Dynamic Model 2. Part of the Christophe et al 2008 Functional-Structural Plant Model 3. Chew et al 2012 Photothermal Model 4. Salazar et al 2009 Photoperiodism Model &nbsp; To run the
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DALEC (Data Assimilation Linked Ecosystem Carbon) represents the C cycle with a simple box model of pools connected via fluxes. There are five pools: C content of foliage (Cf); woody stems and coarse roots (Cw) and fine roots (Cr); and of fresh leaf and fine root litter (Clitter) and soil organic matter (SOM) plus WD (CSOM/WD).&nbsp; The fluxes among pools are based on the following assumptions:<ol><li> All C fixed during a day is either expended in autotrophic respiration or else
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Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms.&nbsp; &nbsp; Molecular Systems Biology <b>9</b> Article number: 650&nbsp;&nbsp;doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance <i>via</i> CRY signalling controls the <i>Arabidopsis</i>
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Model outputs mRNA expression of PIF4/5 that is under control of&nbsp;the Pokhilko extended&nbsp;circadian clock. The first version (Model&nbsp;2a in the supplementary file)&nbsp;has inhibition of PIFs from TOC1.&nbsp;The second version (Model 2c) has PIF activity promoted by LHY/CCA1 - this is currently the most accurate model when compared to data. Models shall be updated later to include PIF4/5 protein levels. Parameter values for this and other External Coincidence models
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Model that eliminates several light inputs. RVE8, NOX are incorporated. Individual representation of CCA1 and LHY. Several changes in conections and light inputs. Fogelmark reports eight parameter sets. This SBML file contains the first parameter set <br><br><strong>Related Publications</strong></strong><br>Fogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from:
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SBGN model of glycolysis<br><br><strong>Originally submitted to PLaSMo on 2012-03-05 11:43:15</strong></strong>

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sbgn model of signalling<br><br><strong>Originally submitted to PLaSMo on 2012-03-05 11:53:41</strong></strong>

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"LINTUL simulates potential growth of a crop, i.e. its dry matter accumulation under ample supply of water and nutrients in a pest-, disease- and weed-free environment, under the prevailing weather conditions. The rate of dry matter accumulation is a function of irradiation and crop characteristics. The model makes use of the common observation that the crop growth rate under favourable conditions is proportional to the amount of light intercepted (Monteith, 1977). Dry matter production is,
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This is a verified version of the model named &nbsp;LINTUL&nbsp;in this repository. The model is verified against the benchmark FST implmmentation. LINTUL assumes&nbsp;non-limiting conditions. See the "LINTUL" model entry in this repository for a description<br><br><strong>Originally submitted to PLaSMo on 2011-02-23 00:08:23</strong></strong>

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This version is derived from a model from the article: <strong>Extension of a genetic network model by iterative experimentation and mathematical analysis. </strong>Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ <em>Mol. Syst. Biol. </em>2005; 1: 2005.0013 <a href="http://www.ncbi.nlm.nih.gov/pubmed/16729048">16729048</a>, &nbsp;SBML model of the interlocked feedback loop network The model describes the circuit
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This is a version derived from a model from the article: <strong>Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. </strong> Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ <em>Mol. Syst. Biol.</em>2006;Volume:2;Page:59 <a href="http://www.ncbi.nlm.nih.gov/pubmed/17102804">17102804</a>, &nbsp; The model describes a three loop circuit of the Arabidopsis
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Test by Martin for simileXML<br><br><strong>Originally submitted to PLaSMo on 2012-03-08 11:39:23</strong></strong>

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This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration. &nbsp; In the original paper, the model is used twice, once for the trees and once for the grass under the trees, with the grass receiving light not intercepted by the trees. &nbsp; The model provided here is just for a single vegetation component.<br><br><strong>Related Publications</strong></strong><br>McMurtrie
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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
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Model files accompanying Seaton et al., Molecular Systems Biology, 2015 Abstract: Clock?regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best?understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN?BINDING, KELCH REPEAT, F?BOX 1 (FKF1) transcription.
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This is a modified version of Biomodels89, containing a light-forcing function. This variant is configured to run cycles of LD8:16<br><br><strong>Related Publications</strong></strong><br>ocke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ. (2006). Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. . Mol Syst Biol . <br><br><strong>Originally submitted
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Neuronal musch signalling sbml diagram<br><br><strong>Originally submitted to PLaSMo on 2012-03-05 12:33:43</strong></strong>

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&nbsp;This model is derived from Biomodels 299 - the Leloup et al Neurospora clock model. This variant contains an embedded light-forcing function (SBO:000475) that provides a periodic light input. In this model, after 72h of LD12:12, the amplitude of Vs ( the light dependent parameter ) increases to 4.1, leading to chaotic oscillations. For this to happen, the periodic light function needs to produce a square-wave pattern.&nbsp;&nbsp;&nbsp; Execution of this model will result in
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This model, derived from Biomodels299, is a variant of the Neurospora Circadian clock model of Leloup et al., 1999. It is supplemented with a periodic light function (SBO:0000475) that is parameterized to produce sinusoidal oscillations in the light sensitive parameter Vs with an amplitude of 5. These sinusoidal wave-form maintains entrained oscillations even with high light input, and is described in Figures 6 and 7 of Gonze and Goldbeter, 2000.<br><br><strong>Related
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Draft of MEP pathway for isoprenoid synthesis, created 2012-2013 by Oender Kartal in the Gruissem lab. He notes "It contains some annotations and references for the parameter values and rate equations and produces a stable steady state, so you can do some control analysis. It simulates day-metabolism, since the MEP Pathway is supposedly active during the day." Unpublished, for use by TiMet consortium only.<br><br><strong>Originally submitted to PLaSMo on 2013-09-13
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Andrew's work-in-progress P2012 version. <strong>NB KNOWN PROBLEMS</strong> do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.<br><br><strong>Originally submitted to PLaSMo on 2013-02-26 17:23:01</strong></strong>

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This is part of the GreenLab Functional-Structural Plant Model for Arabidopsis published in Christophe et al 2008. This model was re-factored, to facilitate the integration in the Chew et al Framework Model, and it cannot be run as a standalone model.&nbsp; <br><br><strong>Related Publications</strong></strong><br>Angélique Christophe A E, Véronique Letort B, Irène Hummel A, Paul-Henry Cournède B, Philippe de Reffye C, Jérémie Lecœur (2008). A model-based
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To check if all works fine after struts update. Checking editorial options<br><br><strong>Additional Attributes</strong></strong><br>tested: <p>
Yes, against schema</p>
<br><br><strong>Originally submitted to PLaSMo on 2013-11-22 15:15:40</strong></strong>

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The model is an extensio of PLM_67v3 with an additional an additional variable Temp in ODE 25. This change allows to simulated warm pulses that affect EC stability using COPASI.&nbsp;<br><br><strong>Originally submitted to PLaSMo on 2014-03-10 13:16:25</strong></strong>

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This is the SimileXML for the Salazar model linked to the T6P/TPS pathway (Wahl et al. Science 2013). The Simile version of this model and the parameter file are also attached here. Time series data of T6P and <em>FT</em> mRNA for Col wild type and <em>tps1</em> mutant from Fig. 1 in Wahl et al were used to re-optimise Bco, KCO, kT6P and vT6P (which replaces VCO). <strong>Note:</strong> This set of parameter values has only been optimised and tested for a 16:8
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The model shows how the <em>CONSTANS</em> gene and protein in <em>Arabidopsis thaliana</em> forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (<a
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This is the SimileXML for the Salazar2009_FloweringPhotoperiod model in PlaSMo. It corresponds to Model 3 in the publication of Salazar et al 2009. The Simile version of this model is also attached here. <strong>Instructions to run the Photoperiodism Model in Simile</strong> 1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Save all the files into the same folder. 2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Copy and paste the attached ‘lightfunction.pl’
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Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.<br><br><strong>Related Publications</strong></strong><br>Sorokina et al (2011). BMicroarray data can predict diurnal changes of starch content in the picoalga Ostreococcus.. BMC Systems Biology. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21352558<br><br><strong>Originally submitted to PLaSMo on 2011-08-12 15:34:00</strong></strong>
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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
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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)<br><br><strong>Related Publications</strong></strong><br>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
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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)<br><br><strong>Related Publications</strong></strong><br>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
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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)<br><br><strong>Related Publications</strong></strong><br>Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light
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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)<br><br><strong>Related Publications</strong></strong><br>Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014).
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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)<br><br><strong>Related Publications</strong></strong><br>Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014).
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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)<br><br><strong>Related Publications</strong></strong><br>Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014).
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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)<br><br><strong>Related Publications</strong></strong><br>Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light
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Person responsible: BioData SynthSys

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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)<br><br><strong>Related Publications</strong></strong><br>Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light
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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)<br><br><strong>Related Publications</strong></strong><br>Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light
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Person responsible: BioData SynthSys

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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)<br><br><strong>Related Publications</strong></strong><br> Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014).
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TiMet flower specific protein detection network<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:39:54</strong></strong>

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Trial upload of the pollen netwrok from TiMet<br><br><strong>Originally submitted to PLaSMo on 2012-02-27 12:17:46</strong></strong>

PP interaction network exported from Cytoscape in XGMML<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:32:33</strong></strong>

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Test for root network<br><br><strong>Originally submitted to PLaSMo on 2012-02-27 14:24:59</strong></strong>

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The seed network, uploaded as a test from Cytoscape<br><br><strong>Originally submitted to PLaSMo on 2012-02-24 11:41:50</strong></strong>

Cytoscape shoot specific diurnal transcript oscillation.<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:42:30</strong></strong>

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Cytoscape silqueue specific protein detection<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:44:13</strong></strong>

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"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
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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).<br><br><strong>Originally submitted to PLaSMo on 2010-05-04
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Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.<br><br><strong>Related Publications</strong></strong><br>Wilczek
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