Chew_et_al_2014_Framework_Model - PLM_76, version 1

This is the Framework Model (Chew et al, PNAS 2014; <a href=""></a>) 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

<a href=""></a>


<strong>Instructions to run the Framework Model in Simile (updated 2 Dec 2014)</strong>


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.  


           (<strong>NOTE:</strong> 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:).


          (<strong>NOTE: </strong>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 ‘’ file in the following folder (or Mac equivalent):              


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


        (<strong>NOTE: </strong>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


           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


           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.



<strong>Input variables:</strong>







<strong>Some useful parameters:</strong>

JV ratio (Jmax/Vcmaxratio)

Starch turnover


<strong>Some relevant output variables:</strong>



Shoot DW (shoot dry weight in g)

Shoot FW (shoot fresh weight in g)

Root_mass (root biomass in g)


<strong><em>Carbon pools:</em></strong>

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)


<strong><em>Gas exchange:</em></strong>

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) 

Originally submitted to PLaSMo on 2013-11-12 16:05:47


Modelling Analysis

BioData SynthSys

Projects: PlaSMo model repository

Investigation: Existing models that were re-factored and integrated into the Arabidopsis Framework Model (AtFM)

Study: Chew_et_al_2014_Framework_Model - PLM_76

Assay position:

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

help Creators and Submitter
Additional credit

Yin Hoon


Views: 1200

Created: 10th Jan 2019 at 17:40

Last updated: 7th May 2019 at 13:24

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