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Arabidopsis leaf carbohydrate model (Rasse and Tocquin)

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2010-01-27 12:50:25.0

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 equivalents across 24 days of simulation. Thus, the validation was not done against the values the original FORTRAN wrote to disk data files. The loops for CO2 and light intensity in the code were set to start and stop at 36 and 120 respectively (i.e. only one value for each was used in the validation). The original code and the Simile model gave exactly the same values for all the state variables for the wild type and the two mutants even after a full 24 days of simulation. Comments on numerical integration: The model should be run using Euler integration with a time step of 1 unit. Comments on running the Simile model: The user can adjust the length of the day light period using the variable "light_hr" and the number of iteration steps per hour using "steps per hour", both are in the Simile submodel "time control". Note that the Simile model was only validated using 600 steps per hour as was used in the main reference.

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arabidopsis_clock_biopepa

Format: SBML L2 V3

Contact/Model Admin: mguerrie

Submission Date: 2011-09-08 17:35:44.0

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.

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Arabidopsis_clock_extend

Format: SBML L2 V3

Contact/Model Admin: amillar2

Submission Date: 2010-05-04 11:20:49.0

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 to 0 and "dusk" to 12 in the light function.

The third version has parameters "dawn" and "dusk" in equation for light function, which allows to simulate various photoperiods by changing parameter "dusk".

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Arabidopsis_clock_P2011

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2012-03-07 12:15:12.0

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 to version 1 of this model (the published SBML is correct).

 The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including:

  1. the Evening Complex genes (ELF4, ELF3, LUX),
  2. light-regulated degradation of ELF3 by COP1,
  3. TOC1 as a repressor rather than an activator of LHY/CCA1.

These changes allowed the removal of hypothetical components TOC1mod (or X) and Y from the earlier models. They also reveal that the central loop of the model is a triple-repressor ring oscillator, or 'repressilator' (illustrated in Fig. 8, GIF attached).

SBML curation notes (please see Comments for each version): Compared to the model version submitted to the Biomodels database, version 1 here slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. A MATLAB version is attached to version 1. In version 2, the rule is used with a generic SBML StepFunction (Adams et al. J. Biol. Rhythms Aug 2012) to describe the light-dark cycle more flexibly. Versions 1 and 2 have multiple sinks and sources created by CellDesigner. These are removed in versions 3 & 4. Version 3 has the published lightfunction, and an equivalent COPASI file attached. Version 4 has the StepFunction.

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Arabidopsis_clock_P2012

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2013-04-03 20:23:37.0

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 repressor of multiple clock genes, rather than only of LHY/CCA1.
  • ABAR transcription modified by TOC1, affecting stomatal aperture.
  • TOC1 transcription modified by ABA.

Notes on the paper

In 2018, Daewook Kim made us aware of a likely typo in the printed version of the model equations in the paper, where the term (A_0+c^m_ABAR+g29) in the last equation about c_AR lacks a ^2.

i.e. Sqrt[ (A_0+c^m_ABAR+g29)-4A_0c^m_ABAR) ] -> Sqrt[ (A_0+c^m_ABAR+g29)^2 -4A_0c^m_ABAR) ].

SBML curation notes (please see Comments for each version):

version 1 here is the version published as Supplementary Information and submitted to the Biomodels database.

Copasi and MATLAB versions are attached to version 1.

NB. Use only 'v1' Matlab files. Matlab files named 'v0' have older parameter values for parameters g4, g23, g25, m6, m23, m24, though these differ only slightly. The Copasi version is the same as the published SBML version, and the 'v1' matlab files.

This model has formed the basis for further work by external groups, as described in the following links:

Fogelmark et al. PLoS CB 2014 - http://dx.doi.org/10.1371/journal.pcbi.1003705

Zhou et al. Nature 2015 - http://dx.doi.org/10.1038/nature14449

Foo et al. PLoS CB 2016 - http://dx.doi.org/10.1371/journal.pcbi.1004748

Calluwe et al. Frontiers 2016 - http://dx.doi.org/10.3389/fpls.2016.00074

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AuxSim full

Format: SimileXMLv3

Contact/Model Admin: amillar2

Submission Date: 2011-01-11 20:52:13.0

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 protoplasts for different cell sizes and AUX/LAX auxin carrier distributions.

Note that the working version of the model is in the Simile (.sml) version rather than in XML (which is a temporary holding dummy file). 

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C3 photosynthesis (Farquhar, von Caemmerer, Berry) model

Format: SimileXMLv3

Contact/Model Admin: cdavey

Submission Date: 2010-01-27 12:41:44.0

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.

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Central plant metabolism

Format: SBGN-ML PD

Contact/Model Admin: mbbeaton

Submission Date: 2012-03-05 11:52:18.0

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 more

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CENTURY_Rowe_daily

Format: SimileXMLv3

Contact/Model Admin: robertm

Submission Date: 2010-10-28 14:19:26.0

"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 the model's compartments. The minimum configuration of elements is C and N for all the model compartments. The organic matter structure for carbon(C), nitrogen(N), phosphorus(P) and sulfor(S) are identical; the inorganic components are computed for the specific inorganic compound."  [Source: CENTURY 4 home page: http://www.nrel.colostate.edu/projects/century/] 

This Simile implementation of the CENTURY model was made by Ed Rowe based on a Stella re-implementation of the soil component of the CENTURY model made by Georg Cadisch. The unit of time is day.   Note that no check has been made of the correspondence between these models and any of the official implementations. 

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Chew_et_al_2012_Photothermal_Model

Format: SimileXMLv3

Contact/Model Admin: yinhoon

Submission Date: 2013-11-12 14:47:20.0

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’ (triangle) button

3.       When you run the model for the first time, you will be prompted to enter the value of temperature, sunrise and sunset times (in 24-hour format)

4.       The time unit and time step also need to be adjusted as follows:

           a.       The time step can be set in the run display window. The time step #1 should be set to 1

           b.      The time unit should be changed to ‘hour’, which can be done in the ‘Run settings’ tab in the run display window

5.       Model execution time can be set in the run display window. However, even if a high value is used, model will still stop execution at the predicted flowering time.

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Chew_et_al_2014_Framework_Model

Format: SimileXMLv3

Contact/Model Admin: yinhoon

Submission Date: 2013-11-12 16:05:47.0

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

 

Instructions to run the Framework Model in Simile (updated 2 Dec 2014)

 

1.       Download the 'Simile version of the Framework Model' zip folder  from PlasMo (the

           last entry in the Supplementary Data Files at the bottom of the model record), and

           extract the files into a single folder. 

           

          On Windows, a good choice is the C:\[user filepath]\Documents\My Simile Files\

           directory that is created during installation.  

          

           (NOTE: the \My Simile Files\ directory might not be in your normal home directory

           location, e.g. if your home directories are mapped to a drive other than C:).

 

          (NOTE: the PlasMo repository adds a number to the start of all filenames; if you

          download individual files instead of the ZIP archive, please edit the filenames and

          remove the numbers).  

 

2.       Copy and paste the ‘DiscXYZ.tcl’ file in the following folder on Windows (or the

          equivalent in the installation directory you selected on a Mac):              

         

          Windows:        Program Files > Simile6.0 (or other software version) > IOTools

         

          Mac: Go to Applications folder and right click on the Simile icon, and then click 'Show

                    Package Contents'. Then go to the following:

                    Contents > Resources > IOTools

 

         Linux: /usr/lib/simileXX/IOTools           

          

3.       Copy and paste the ‘lightfunction.pl’ file in the following folder (or Mac equivalent):              

         

                    Program File > Simile6.0 (or other software version) > Functions   

 

        (NOTE: If you do not have Admin privileges on your computer, you can create IOTools  

        and Functions subdirectories in your local user files, under the Documents\My Simile

        Files\ directory mentioned in step 1 above. Paste the files in Step 2 and 3 above into

        the appropriate subdirectories)  

 

4.       Start the Simile software, then open the 'Framework Model.sml' file in the folder where

           you saved it.  

 

5.       To run the model:            

           a.       Model > Run or click on the ‘Play’ (triangle) button  

 

6.       When you run the model for the first time, you will be prompted to load the parameter

          file. To do so:            

          a.       Load the ‘Framework model.spf’ file at the TOP LEVEL and click OK.  

 

7.       The time unit and time step should be correct, but might need to be adjusted as

           follows:            

           a.       The time step can be set in the run display window. Two time steps are used in

                      the model. Time step #1 should be set to 1, while time step #2 should be set to

                      0.001             

           b.      The time unit should be changed to ‘hour’, which can be done in the ‘Run

                     settings’ tab in the run display window  

 

8.       To use the visual animation tool, the configuration file can be loaded in the run

           display window:            

           a.       File > Load configuration… > Select ‘Framework model.shf’  

 

9.       Model execution time can be set in the run display window. However, even if a high

          value is used (e.g. 1000 hours), the model will still stop execution at the predicted

          flowering time.

 

 

Input variables:

co2

Sunrise

Sunset

Temperature

light

 

Some useful parameters:

JV ratio (Jmax/Vcmaxratio)

Starch turnover

 

Some relevant output variables:

 

Biomass:

Shoot DW (shoot dry weight in g)

Shoot FW (shoot fresh weight in g)

Root_mass (root biomass in g)

 

Carbon pools:

leaf_c_perplant (Total g Carbon in the shoots)

root_c_perplant (Total g Carbon in the roots)

sta_c_perplant (Total starch in g Carbon)

suc_c_perplant (Total sucrose in g Carbon)

 

Gas exchange:

al_pt_plantassim (photosynthesis in g Carbon per plant per hour)

rlc_pt1 (Growth respiration from leaves in g Carbon per plant)

rrc_pt1 (Growth respiration from roots in g Carbon per plant)

leaf respper plant (Maintenance respiration from leaves in g C per plant)

rrm_pt (Maintenance respiration from roots in g C per plant) 

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DALEC

Format: SimileXMLv3

Contact/Model Admin: robertm

Submission Date: 2010-11-02 10:27:31.0

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:

  1. All C fixed during a day is either expended in autotrophic respiration or else allocated to one of three plant tissue pools – foliage, wood, or fine roots.
  2. Autotrophic respiration is a fixed fraction of total photosynthetic fixation, and it is not directly temperature sensitive.
  3. Plant allocation and litterfall are donor-controlled functions with no direct environmental influence and constant rate parameters.
  4. Soil transformations are sensitive to temperature, with a Q10 of 2.0. Otherwise, the only environmental forcing in the C model is on GPP, via solar radiation, air temperature, and soil moisture.
  5. All C losses are via mineralization; there is no dissolved loss term.

The aggregated canopy model (ACM) of photosynthesis (Williams et al., 1997) provides the forecast estimate of daily C inputs to the system. The ACM is a big-leaf, daily time step model that estimates GPP as a function of LAI, foliar nitrogen, total daily irradiance, maximum and minimum daily temperature, day length, atmospheric CO2 concentration, soil–plant water potential, and total soil–plant hydraulic resistance. The model has 10 parameters.  

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DomijanTS_AtClock2011

Format: SBML L2 V4

Contact/Model Admin: amillar2

Submission Date: 2012-01-11 10:23:00.0

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.2013.7

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Glycolysis SBGN

Format: SBGN-ML PD

Contact/Model Admin: mbbeaton

Submission Date: 2012-03-05 11:43:15.0

SBGN model of glycolysis

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Insulin-like growth factor signaling

Format: SBGN-ML PD

Contact/Model Admin: mbbeaton

Submission Date: 2012-03-05 11:53:41.0

sbgn model of signalling

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LINTUL

Format: SimileXMLv3

Contact/Model Admin: robertm

Submission Date: 2010-01-27 13:53:11.0

"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, therefore, modelled as the product of light interception and a constant light use efficiency. The dry matter produced is partitioned among the various plant organs, using partitioning factors defined as a function of the phenological development stage of the crop. The dry weights of the plant organs are obtained by integration of their growth rates over time." (Source: LINTUL documentation)

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LINTUL_V2

Format: SimileXMLv3

Contact/Model Admin: jmassheder

Submission Date: 2011-02-23 00:08:23.0

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

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Locke2005_CircadianClock_tanh

Format: SBML L2 V1

Contact/Model Admin: amillar2

Submission Date: 2010-05-05 14:54:28.0

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 production rates of the following species: LHY mRNA (cLm), cytoplasmic LHY (cLc), nuclear LHY (cLn), TOC1 mRNA (cTm), cytoplasmic TOC1 (cTc), nuclear TOC1 (cTn),X mRNA (cXm), cytoplasmic X (cXc), nuclear X (cXn), Y mRNA (cYm), cytoplasmic Y (cYc), nuclear Y (cYn), nuclear P (cPn).

Compared to the original version in Biomodels database, BIOMD0000000055.xml.origin, this version uses a better description of the light-dark cycle, by Drs. Ozgur Akman and Kevin Stratford. The model contains a candidate for a community-standard cyclic function, which uses tanh functions to achieve rapid yet numerically continuous steps from light to darkness, rather than discrete events in SBML.

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Locke2006_CircadianClock_tanh

Format: SBML L2 V1

Contact/Model Admin: amillar2

Submission Date: 2010-05-12 17:38:15.0

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 mRNA (cLm), cytoplasmic LHY (cLc), nuclear LHY (cLn), TOC1 mRNA (cTm), cytoplasmic TOC1 (cTc), nuclear TOC1 (cTn), X mRNA (cXm), cytoplasmic X (cXc), nuclear X (cXn), Y mRNA (cYm), cytoplasmic Y (cYc), nuclear Y (cYn), nuclear P (cPn), APRR7/9 mRNA, cytoplasmic APRR7/9, and nuclear APRR7/9.

The paper describes the behaviour of the model in constant light (LL) and day-night cycles (LD). The version curated on Biomodels had no LD input, allowing only simulation in LL conditions: BIOMD0000000089.xml.origin.

The version uploaded here uses a better description of the light-dark cycle, by Drs. Ozgur Akman and Kevin Stratford. The model contains a candidate for a community-standard cyclic function, which uses tanh functions to achieve rapid yet numerically continuous steps from light to darkness. The SBML file was validated by CSBE, including by Dr. Richard Adams.

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McMurtrie vegetation model

Format: SimileXMLv3

Contact/Model Admin: robertm

Submission Date: 2010-06-15 15:56:57.0

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.

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