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.

Version 1.2.3 of Sap Flow Tool has been released.

What’s new in this version:

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.

PhytoSim 1.2.1 has been released. This is a maintenance release which improves the stability of the login and module manager system. Make sure you upgrade to this version in order to avoid future problems logging in and installing module updates. No modules need to be re-installed.

Direct download links: Windows and Mac.

Ever wondered what the uncertainty of your model predictions is? Using the NEW PhytoSim Uncertainty Analysis module you will be able to find out just that.

An uncertainty analysis allows propagating parameter, initial condition and/or input uncertainties through the model to obtain the model output uncertainty. Setting up the analysis requires almost no work, just assign the source uncertainties, select the number of model evaluations and you are good to go. The well-known Monte Carlo technique is used to propagate the uncertainties and Latin Hypercube sampling is used to ensure that the uncertainty distributions are sampled evenly.

Screenshot of a source uncertainty while it’s being sampled:

Screenshot of the model output uncertainty (maximum, 95th percentile, mean, median, 5th percentile and minimum of the distribution):

For more information have a look at the PhytoSim Uncertainty Analysis User Guide webpage.

Pricing: Free for now (beta period will last until the end of 2011), afterwards 499 EUR.

Installation:

• Make sure you have the latest PhytoSim version.
• Select the Uncertainty Analysis module in the PhytoSim module manager and select ‘Install module’ from the toolbar.

Probably the most important aspect of any modelling study is knowing which of your model parameters (and/or initial conditions) contribute most to the model output. As of today, such analysis is possible in PhytoSim.

The PhytoSim Sensitivity Analysis module offers 3 types of information:

Dynamic sensitivity functions: Shows how small changes in model parameters change the model output. By analyzing the sensitivity functions you will get a tremendous insight into your model.

Importance ranking: Ranks the model parameters according to their influence on the model output and shows this on a nice bar chart.

Identifiability analysis: Use the intuitive user interface to find out which parameter combinations can be estimated based on a given set of measurements. You can even do the analysis before any real data is collected.

For more information have a look at the PhytoSim Sensitivity Analysis User Guide webpage.

Pricing: Free for now (beta period will last until the end of 2011), afterwards 499 EUR.

Installation:

• Make sure you have the latest PhytoSim version.
• Select the Sensitivity Analysis module in the PhytoSim module manager and select ‘Install module’ from the toolbar.

Version 1.2 of PhytoSim has been released. This release comes with updates for following modules: Data I/O, Modelling, Simulation and Calibration.

Download the Windows version here and the Mac version here.

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

Key new features:

• Work offline on the Mac.
• ‘Remember me’ option when logging in.
• Data I/O:

• Use date/time in outputs (converts from decimal time).
• New output type: matrix file. Can contain matrix output from various PhytoSim modules.
• Modelling:

• New nounit( x ) function: returns the value of x without a unit, where x is a model component.
• New pi() function: returns the number pi.
  WARNING: models having a ‘pi’ variable will now be invalid. Please replace these with ‘pi()’.
• Multi-line comments. Use: ‘/*’ and ‘*/’ to enclose multiple lines of comments.
• Added Collapse/Expand to the model navigator context menus to quickly expand/collapse the model tree.
• New model: HydR, linking diameter changes to radial water transport across a radial hydraulic resistance (Steppe et al., 2011). Only available for non-trial accounts.
• Simulation:
• Added the ability to put all model component values to their defaults and/or initial values.
• Added Collapse/Expand to the model navigator context menus to quickly expand/collapse the model tree.
• Calibration:
• Confidence information calculations: estimation errors and correlation matrix.
  
• ‘Single shot’ optimizer: evaluate the objective at the initial values.
• ‘Best’ simulation curve now has a +/- 2*stdev measurement uncertainty band on it.
• Minimum and maximum graph marker lines for optimizer variables.

For a more detailed list of all new features, changes and bug fixes see:

• PhytoSim change log
• Data I/O change log
• Modelling change log
• Simulation change log
• Calibration change log

Version 1.2.2 of Sap Flow Tool has been released.

What’s new in this version:

Phyto-IT was present at the 8th International Workshop on Sap Flow in Volterra, Italy. At the booth of ICT International a demo video of Sap Flow Tool was shown throughout the conference.

Pictures of the sponsors area where the Sap Flow Tool demo video was shown:

A short article about Phyto-IT appeared in the April issue of ‘Ondernemers Oost-Vlaanderen’, a monthly magazine about the East-Flanders business world. Read the article here (in Dutch).