Archive for the ‘PhytoSim’ Category

PhytoSim 2.1 released

Wednesday, December 16th, 2015

PhytoSim 2.1 has been released. Just in time for the Christmas holidays. All trials have been reset, so everyone who previously created an account can try out this version as well (first download the new version).

Install it using the internal PhytoSim updater or download it from the PhytoSim download page.

This version includes some great new features:

  • Simulation module:
    • Ability to choose the display time unit
  • Calibration module:
    • Moving window calibration: Automatically fit a model to parts of the data using a moving window approach resulting in calibrated values for each time window.
    • Ability to enable/disable optimizer and/or objective variables
  • Sensitivity analysis module:
    • Morris screening global sensitivity analysis: This method is a well known global sensitivity analysis screening technique which is able to detect, using a limited number of model simulations, which model components have (a) linear and additive or (b) non-linear and interaction effects.
    • Extended FAST global sensitivity analysis: The Extended Fourier Amplitude Sensitivity Test is a variance based global sensitivity analysis technique. By decomposing the model output variance, this method is able to calculate first order sensitivity indices and total sensitivity indices. The total sensitivity indices, as the name suggests, quantify the total sensitivity of a model component, including the interactions with other components.
    • Ability to enable/disable source and/or target components
  • Uncertainty module:
    • Ability to enable/disable source and/or target components

Some things have been changed as well:

  • Calibration module: calibration data is only shown between start and stop time

Finally, many bugs were fixed. Some of them are:

  • Data I/O module: problem importing data files with old-style Mac file endings
  • Simulation module: curve legend item not visible when dragging a model component on the graph
  • Simulation module: unable to edit x-axis minimum when autoscaling is turned off
  • Uncertainty module: progress bar does not reset when starting a new analysis

Happy simulating!

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PhytoSim used for the ‘Modelling drought stress responses’ COST Training School

Friday, May 30th, 2014

31 enthusiastic Early Stage Researchers used PhytoSim during a 3-day COST Training School to learn about modelling and simulation and applied this knowledge to investigate drought stress responses in trees. During the course, PhytoSim was used for teaching and hands-on exercises.

The ‘Modelling drought stress responses’ COST Training School was organised by the UGent Laboratory of Plant Ecology from May 26th-28th 2014.


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PhytoSim 2.0.1 Released

Thursday, May 8th, 2014

PhytoSim 2.0.1 has been released. Download it here.

Due to internal encryption changes, remembered login passwords might not work anymore. If you experience login issues, please retype your password in the password field of the login dialog.

This is a bug fix release which fixes following issues:


  • FIXED: Crash when transferring calibrated source component (e.g. parameters) values to the Simulation Module.
  • FIXED: Simulation graph curve settings issue for curves on the second Y-axis.
  • FIXED: Issue with PhytoSim folder location in Preferences.
  • FIXED: Issue with simulation Data Variables not updating their value when selecting them in the navigator.


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PhytoSim 2.0 Released

Tuesday, June 25th, 2013

Version 2.0 of PhytoSim has been released. Download it here.

These are the new features/changes and fixes:


  • CHANGED: Simplified Module Manager, all modules are now built-in (faster startup, no additional downloads required).
  • CHANGED: New PhytoSim software update mechanism.
  • CHANGED: The Help > Support dialog has been removed. Contact for support related questions.
  • CHANGED: Support for multiple simultaneously running PhytoSim instances per account (default is still 1 instance).
  • FIXED: Mac OS X Snow Leopard is supported again.
  • FIXED: Bug for workspaces within a folder structure with folder names containing special characters.

 Data I/O Module:

  • NEW: Embedded data input type. Embed data directly in the workspace: enter manually, copy-and-past or drag-and-drop selected data from text files or Excel).

 Modelling Module:

  • NEW: Fractional units, e.g. cm^3/2.
  • NEW: New unit ‘#’, representing a count or a number of items. E.g. 20 #[plants].m^-2[ground].
  • NEW: New crop model: SUCROS1 (Simple and Universal CROp growth Simulator).
  • CHANGED: The valueat( x, at ) function for data variables now uses the data variable independent variable for the ‘at’ argument instead of the model independent variable.
  • FIXED: Sort order violation for algebraicVariable = previous( algebraicVariable ) or valueat( algebraicVariable, t ).

 Simulation Module:

  • NEW: Graph curves can be put on the second Y-axis.
  • NEW: Logarithmic scales on the Y-axes.
  • NEW: SUCROS1 crop model example showing embedded data inputs and advanced use of the valueat() function.
  • FIXED: Scroll wheel zooming no longer zooms out beyond the graph data.
  • FIXED: Potential crash when zooming in on graphs.

 Calibration Module:

  • CHANGED: Faster calibration when the simulation period is only a small part of the available data period.
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PhytoSim @ HortiModel 2012

Friday, November 16th, 2012

Phyto-IT demonstrated its PhytoSim modelling and simulation software at the HortiModel 2012 conference (Nanjing, China, November 4-8, 2012).

The HortiModel 2012 conference was the Fourth International Symposium on Models for Plant Growth, Environmental Control and Management in Protected Cultivation. It covered a wide range of topics related to horticulture:

  • Crop and Climate Management
  • Water, Nutrient and Energy Management
  • Decision Support and Farm Management
  • Product Quality
  • Systems Biology, Gene-plant-crop Modelling
  • 3D-models, Architectural Models
  • Methodological Issues, Aggregation and Scale
  • Combination of Models and Sensors

HortiModel 2012

HortiModel 2012 booth

Thanks to all the participants who came by our booth!

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PhytoSim v1.3 Released [UPDATED]

Wednesday, August 22nd, 2012

Version 1.3 of PhytoSim has been released. This release comes with updates for all modules: Data I/O, Modelling, Simulation, Calibration, Sensitivity and Uncertainty.

Download it here (WARNING: Mac OS X Snow Leopard is no longer supported). Install the new version and update the modules in the Module Manager.

[UPDATE] If you are experiencing problems updating the Simulation module, delete the PhytoSimSimulation folder in: “My Documents/PhytoSim/Modules” and continue updating the other modules.

For this occasion, all trial accounts have been reset enabling everyone to try out the new release.

Key new features:

  • User Guide search (Help > User Guide; search field is located at the top).
  • The current workspace can now be closed (File > Close).
  • Data I/O
    • Titles and units of input columns can now also be edited by clicking a settings button in the header of a selected input column.
  • Modelling:
    • Added support for unit substances, e.g. cm^3[H2O].g^-1[leaf].
    • New modelCarbohydrateSupplyDemand, carbohydrate supply and demand model for vegetative growth, Gent and Seginer (2012).
    • New functionvalueat( variable, at ), returns the value of a variable at any past time.
    • New functionaverage( variable, from, to ), returns the average of a variable between two points in time.
    • New functionintegral( variable, from, to ), returns the integral of a variable between two points in time.
    • New functionuniform( minimum, maximum ), returns a uniformly distributed random number.
    • New functiontriangular( minimum, mode, maximum ), returns a triangularly distributed random number.
    • New functionnormal( mean, stddev ), returns a normally distributed random number.
    • New functionpoisson( mean ), returns a poisson distributed random number.
    • Parentheses matching in the model editor.
    • Units in equations are no longer automatically converted: stricter but less confusing! As a consequence, unit conversion warnings no longer show up. WARNING: If you relied on automatic unit conversions in your models, they will not be valid anymore. Inserting the proper unit conversion factors will fix this.
  • Simulation:
    • New solver: CVODE stiff/non-stiff differential equation solver (Settings > Solver).
    • New exampleStiff, shows off the benefits of the CVODE solver for stiff differential equations (in Examples/PhytoSimSimulation/Misc).
    • New exampleCarbohydrateSupplyDemand, simulation example for the new CarbohydrateSupplyDemand model (in Examples/PhytoSimSimulation/Plant Physiology).
    • New exampleRandom, illustrates the random number generation functions (in Examples/PhytoSimSimulation/Misc).
    • New exampleExpDecay, illustrates the valueat, average and integral functions (in Examples/PhytoSimSimulation/Misc).
    • Option to turn off curve painting optimization (Graph Settings > Curves). Only needed in some rare cases.
    • A warning is given when no plot interval (Settings > Graphs) is set: protects against too many curve points.
  • Calibration:
    • New global optimizerShuffled Complex Evolution.
    • New global optimizerSimulated Annealing.
    • New global optimizerRandom Search.
    • New exampleSixHumpCamelBack, global optimizer test function (in Examples/PhytoSimCalibration/SixHumpCamelBack).
  • Uncertainty:
    • New uncertainty distribution type: normal distribution.
  • Sensitivity:
    • Data variables can now also be used as source components (like parameters and initial values of derived variables).
    • Setting to turn off numerical error checking (workspace specific).
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Updated PhytoSim simulation and calibration modules available

Thursday, April 19th, 2012

Updated PhytoSim Calibration (v1.2.2) and Simulation (v1.2.1) modules are available. These updates fix a problem with missing Data I/O data when starting a simulation or calibration.

To install the new modules start PhytoSim, head to the Module Manager and update the Simulation and Calibration modules. Also make sure you have upgraded to the latest PhytoSim version (v1.2.2).

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Updated PhytoSim available (v1.2.2)

Monday, April 9th, 2012

PhytoSim has been updated to solve an issue that didn’t allow updating trial modules without purchasing depending modules.

The new version can be found at the PhytoSim download page.

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Updated PhytoSim calibration module available (v1.2.1)

Friday, February 10th, 2012

An update of the PhytoSim calibration module is available (v1.2.1). This release fixes a bug on Windows that caused the application to become unresponsive when plotting a large number of infinite objective values on the “Objective Value vs. Evaluation Number” graph.

The calibration objective is given an infinite value when the optimizer tries to run a model evaluation (simulation) with optimizer variable values on or outside the allowed bounds. These values are plotted on the objective graph as vertical lines (see screenshot). It is normal that the optimizer occasionally ventures close to, or over the bounds. However, if the optimizer repeatedly tries to run evaluations with “illegal” optimizer variable values, it might be an indication  that the optimum is located outside the optimizer variable bounds. If that is the case, the bounds of the optimizer variables which are causing the problem should be relaxed, always keeping in mind that they should still make physical sense.

To install the new module start PhytoSim, head to the Module Manager and update the calibration module.

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Just released: PhytoSim Uncertainty and Sensitivity Analysis v1.0

Monday, January 23rd, 2012

After a few months of beta, today the PhytoSim Uncertainty Analysis and Sensitivity Analysis reached their first stable version (v1.0). As of this release, both modules are no longer free to use, but as always, a 30-day free trial is available for both of them.

Compared to the beta version, only minor changes were made to the Uncertainty Analysis module. However, the new Sensitivity Analysis module does come with a few important new features:

  • Visualisation of the simulation results used for the sensitivity calculations. Access through the ‘More Graphs’ toolbar button.
  • Visualisation of the absolute sensitivities for each source and target component combination. Access through the ‘More Graphs’ toolbar button.
  • The progress bar now also shows the identifiability analysis progress.
  • The identifiability analysis is stopped once a subset size is found for which all subsets are unidentifiable. This greatly reduces the calculation time when a large number of model parameters and/or initial conditions are used in the analysis.

More details about each of the modules (pricing, change log, user guide) can be found on the PhytoSimUncertainty and PhytoSimSensitivity webpages.

To start using the new versions: launch PhytoSim, select the Module Manager and upgrade to the new module versions.

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