Biological problem addressed 'Gene Regulatory Network'

A boolean network was created using booleannet (after experimenting with Squad and CellNetAnalyzer). This network can be simulated and visualized using additional software components that will be part of the pyMantis CMS that is developed by the Translucent project.

RNA timeseries data for Arabidopsis Col wild-type plants and clock mutants, as separate mean and SD files. The raw data is available on BioDare.ed.ac.uk, and is linked as 'Attribution' from elsewhere on FAIRDOMHub.

The starting models are included here in their original forms, the P2011 model as an SBML L3V1 model file, and the KF2014 model of Fogelmark et al. shared as SBML; both prepared by Uriel Urquiza.

This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...

dfds

Version Comments

sdff a fdafafadfafa f f afafaf fd fdfdfd

To check if all works fine after struts update. Checking editorial options

Additional Attributes
tested:

Yes, against schema

"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 ...

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

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 ...

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

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 ...

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 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 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 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 ...

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 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 ...

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

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 ...

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 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 ...

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 tag was back-edited from the correct string to in this file. The file is still correctly opened in VANTED after this modification. The unmodified version is also attached. Related PublicationsFlis et al. (2015). Open ...

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 ...

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 ...

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 ...

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 ...

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

Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412 Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64 ...

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

Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412 Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64 ...

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 ...

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

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.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 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 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 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 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 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 Alexandra's P2011 model with skeleton photoperiod for Graf et al.PNAS 2010.

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

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 ...

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 ...

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 ...

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 ...

This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...

This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...

This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...

This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...

This model is termed P2012 and derives from the article: Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. Alexandra Pokhilko, Paloma Mas & Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It updates the P2011 model from Pokhilko et al. Mol. Syst. Biol. 2012, Plasmo ID PLM_64, by including: TOC1 as a ...

This model is termed P2012 and derives from the article: Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. Alexandra Pokhilko, Paloma Mas & Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It updates the P2011 model from Pokhilko et al. Mol. Syst. Biol. 2012, Plasmo ID PLM_64, by including: TOC1 as a ...

P2011 model from PLM_43 version 6, optimised by Andrew Millar with SBSI PGA optimisation. A limited parameter set were free to optimise over < 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).Originally submitted to PLaSMo on ...

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.

Originally submitted to PLaSMo on 2012-05-31 22:18:27

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.Version Comments Version 2 is the 'public' version with the StepFunction, PLM_64v4. For some reason this was crashing SBSI, but was then cleaned up by passing through Copasi. Thus the file name of this version was Arabidopsis_clock_P2011_exCopasi.xml

This version should be suitable for SBSI optimisation to LD-LL data sets, because it ...

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.

Version Comments

PLM_67v2 set up for LDLL transition at 314h, with wider parameter ranges for most parameters. This is the model file used in LDLL_run2.

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.Version Comments PLM_67v3 model, with TWO stepfunctions. Simulates fine but as of 21 March 2013 did not optimise.

Step2 is usually off because amplitude=0, but can produce LD-DD transition at 262h. To do so, initiate with amplitudeStep1=0 and amplitudeStep2=1.

NB the step1 will still go to LL at 314h, so need to stop DD costing before ...

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.Version Comments Derived from PLM_67v3 - LDLL transition at 314h, with wider parameter ranges, as used in LDLL_run2 - but with one modification 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.

Copasi file also attached. Originally submitted to ...

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.

Version Comments

Corrected m1 parameter and range, tested in SBSI

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 ...

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 ...

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 ...

This is the representation of major parts of the central metabolism in monocotyledon plants. The information has been derived from the MetaCrop [2] database, a manually curated repository of high quality information concerning the metabolism of crop plants. This includes pathways, reactions, locations, transport processes, and moreOriginally submitted to PLaSMo on 2012-03-05 11:52:18

"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.  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, and sulfur through ...

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. Instructions to run the Photothermal Model in Simile 1.       Download the Simile file attached or import the XML into Simile:            a.       File > Import > XML Model Description 2.       To run the model:            a.       Model > Run or click on the ‘Play’ ...

This is the Framework Model (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111) 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   To run the model in Simile, please download the Evaluation Edition of the software from http://www.simulistics.com/products/simile.php ...

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).  The fluxes among pools are based on the following assumptions: All C fixed during a day is either expended in autotrophic respiration or else allocated to one of three ...

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.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Originally ...

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.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Version ...

Model outputs mRNA expression of PIF4/5 that is under control of the Pokhilko extended circadian clock. The first version (Model 2a in the supplementary file) has inhibition of PIFs from TOC1. 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 found in supplementary file.Originally submitted ...

Model outputs mRNA expression of PIF4/5 that is under control of the Pokhilko extended circadian clock. The first version (Model 2a in the supplementary file) has inhibition of PIFs from TOC1. 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 found in supplementary file.Version Comments ...

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 Related PublicationsFogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003705Originally ...

SBGN model of glycolysis

Originally submitted to PLaSMo on 2012-03-05 11:43:15

sbgn model of signalling

Originally submitted to PLaSMo on 2012-03-05 11:53:41

"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, ...

This is a verified version of the model named  LINTUL in this repository. The model is verified against the benchmark FST implmmentation. LINTUL assumes non-limiting conditions. See the "LINTUL" model entry in this repository for a description

Originally submitted to PLaSMo on 2011-02-23 00:08:23

This version is derived from a model from the article: Extension of a genetic network model by iterative experimentation and mathematical analysis. Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ Mol. Syst. Biol. 2005; 1: 2005.0013 16729048,  SBML model of the interlocked feedback loop network The model describes the circuit depicted in Fig. 4 and reproduces the simulations in Figure 5A and 5B. It provides initial conditions, parameter values and rules for the ...

This is a version derived from a model from the article: Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ Mol. Syst. Biol.2006;Volume:2;Page:59 17102804,   The model describes a three loop circuit of the Arabidopsis circadian clock. It provides initial conditions, parameter values and reactions for the production rates of the following species: LHY ...

Test by Martin for simileXML

Originally submitted to PLaSMo on 2012-03-08 11:39:23

Test by Martin for simileXML

Version Comments

Version 2, the product of many seconds of research..

This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration.   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.   The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and ...

This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration.   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.   The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and ...

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 ...

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. ...

This is a modified version of Biomodels89, containing a light-forcing function. This variant is configured to run cycles of LD8:16Related Publicationsocke 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 . Originally submitted to PLaSMo on 2012-03-29 10:24:44

Neuronal musch signalling sbml diagram

Originally submitted to PLaSMo on 2012-03-05 12:33:43

 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.    Execution of this model will result in the behaviour depicted in Figure 2D ...

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.Related PublicationsDidier Gonze and Albert Goldbeter ...

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.

Originally submitted to PLaSMo on 2013-09-13 09:10:53

Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS 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.Comments No parameters constrained in version 1 file. 2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk Compiled successfully in SBSI for optimisation. 2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Version 1 is file P2012_NoSinkNoABAParamsNom38_freshCopasi.xml ...

Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS 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.Comments No parameters constrained in version 1 file. 2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk Compiled successfully in SBSI for optimisation. 2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Version 2 is file P2012_fin_NoABAv4.xml of 6th March.

It ...

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.  Related PublicationsAngélique Christophe A E, Véronique Letort B, Irène Hummel A, Paul-Henry Cournède B, Philippe de Reffye C, Jérémie Lecœur (2008). A model-based analysis of the dynamics of carbon balance at the whole-plant level in Arabidopsis ...

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. 

Originally submitted to PLaSMo on 2014-03-10 13:16:25

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 FT mRNA for Col wild type and tps1 mutant from Fig. 1 in Wahl et al were used to re-optimise Bco, KCO, kT6P and vT6P (which replaces VCO). Note: This set of parameter values has only been optimised and tested for a 16:8 light:dark cycle, and the initial values in the Simile model are for ...

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana 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 (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al., ...

The model shows how the CONSTANS gene and protein in Arabidopsis thaliana 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 (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al., ...

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. Instructions to run the Photoperiodism Model in Simile 1.       Save all the files into the same folder. 2.       Copy and paste the attached ‘lightfunction.pl’ file in the following folder:            Program File > Simile6.0 (or other software version)> Functions 3.       Download the ...

Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.

Related Publications
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

Originally submitted to PLaSMo on 2011-08-12 15:34:00

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 ...

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)Related PublicationsLaura 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 responses to environmental signals. New Phytologist. Originally ...

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)Related PublicationsLaura 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 responses to environmental signals. New Phytologist. Originally submitted to ...

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)Related PublicationsLaura 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 responses to ...

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)Related PublicationsLaura 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 responses ...

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)Related PublicationsLaura 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 responses ...

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)Related PublicationsLaura 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 responses ...

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)Related PublicationsLaura 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 responses to ...

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)Related PublicationsLaura 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 responses to ...

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)Related PublicationsLaura 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 responses to ...

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)Related Publications 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 responses ...

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)Related Publications 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 responses ...

TiMet flower specific protein detection network

Originally submitted to PLaSMo on 2012-03-02 12:39:54

Trial upload of the pollen netwrok from TiMet

Originally submitted to PLaSMo on 2012-02-27 12:17:46

Trial upload of the pollen netwrok from TiMet

Version Comments

Live pollen upload test

PP interaction network exported from Cytoscape in XGMML

Originally submitted to PLaSMo on 2012-03-02 12:32:33

Test for root network

Originally submitted to PLaSMo on 2012-02-27 14:24:59

The seed network, uploaded as a test from Cytoscape

Version Comments

Saving second/third version as a live test

The seed network, uploaded as a test from Cytoscape

Version Comments

Uploading new version for testing

Cytoscape shoot specific diurnal transcript oscillation.

Originally submitted to PLaSMo on 2012-03-02 12:42:30