| Version 2.0 (R2006a+) SimBiology® Software Release Notes | |
This table summarizes what's new in Version 2.0 (R2006a+):
| New Features and Changes | Version Compatibility Considerations | Fixed Bugs and Known Problems | Related Documentation at Web Site |
|---|---|---|---|
| Yes Details below | Yes—Details labeled as Compatibility Considerations, below. See also Summary. | Bug
Reports Includes fixes | No |
New features and changes introduced in this version are:
The Diagram is a graphical user interface you can use to enter model pathways using block representations for species, reactions, and submodels. Use the Plot block to visualize simulation data during a simulation. For a tutorial, see Modeling Using the SimBiology Diagram in the SimBiology Getting Started Guide. You can also access video demos from a list of SimBiology demos.
Find — Type a string in the Find box to quickly find matching model components in the project and in abstract kinetic laws.
Bookmarks — Use complex rules to identify objects from the project, and create a custom and persistent set of desktop and project objects.
In Versions 1.0 and 1.0.1, SimBiology projects saved searches. In Version 2.0, the project saves bookmarks. The software converts a previous version's saved search into a bookmark. After you save a project in Version 2.0, a bookmark is saved and the old search is no longer available. If a project contains a search, you see a warning that the project file will contain a bookmark rather than a search after saving.
All functionality available in Version 1.0 searches are present in Version 2.0 bookmarks except for the ability to mix and match and and or between the search rows. If you have a multiple-row search saved with a mixture of and and or, when you load this project into Version 2.0, it is converted to either all or any based on whether the software first encounters and or or.
You can perform sensitivity analysis using the following properties:
SensitivityAnalysis — Configuration set property that lets you calculate the time-dependent sensitivities of all the species states defined by the StatesToLog property with respect to species initial conditions and parameter values.
SensitivityAnalysisOptions — An object that holds the sensitivity analysis options in the configuration set object. Properties of SensitivityAnalysisOptions are summarized below:
SpeciesInputFactors — Specify the species with respect to which you want to compute the sensitivities of the species states in your model.
ParameterInputFactors — Specify the parameters with respect to which you want to compute the sensitivities of the species states in your model.
Normalization — Specify the normalization for the calculated sensitivities.
For an introduction and an example, see Sensitivity Analysis in the SimBiology User's Guide.
The sbioparamestim function lets you estimate any or all parameters in your model using the experimental data you provide. The software uses the optimization functions in the MATLAB, Optimization Toolbox™, and Genetic Algorithm and Direct Search Toolbox™ software to enable parameter estimation.
Optimization Toolbox and Genetic Algorithm and Direct Search Toolbox software are not required for you to use sbioparamestim. If you do not have these products installed, sbioparamestim uses the MATLAB function fminsearch by default.
For an introduction and an example, see Parameter Estimation in the SimBiology User's Guide.
You can perform ensemble simulations using the stochastic solvers to gather data from multiple stochastic runs of the model. The following functions let you perform ensemble runs:
sbioensemblerun — Performs multiple stochastic ensemble runs of the SimBiology model object.
sbioensembleplot — Shows a 2-D distribution plot or a 3-D shaded plot of the time varying distribution of one or more specified species in the ensemble data generated by sbioensemblerun.
sbioensemblestats — Gets mean and variance as a function of time for all the species in the ensemble data generated by sbioensemblerun.
The sbioconsmoiety function lets you calculate a complete set of linear conservation relations for the species in a SimBiology model object.
For an introduction and an example, see Moiety Conservation in the SimBiology User's Guide.
SimBiology software performs model verification and validation either during simulation, or when you explicitly execute the commands for verification before simulation.
The following new functions let you verify and validate, at the command line, that your model is ready for simulation:
verify — Performs checks on a model to verify that you can simulate the model. You see stacked errors and warnings if any problems are found. To see the entire list of errors and warnings, use sbiolasterror and sbiolastwarning.
sbiolasterror — Returns a SimBiology diagnostic structure array containing the last errors that are generated.
sbiolastwarning — Returns a SimBiology diagnostic structure array containing the last warnings that are generated.
Click the Verify button on the SimBiology desktop toolbar to perform verification and validation of your model. The Output pane opens to show the errors and warnings. You can double-click a result row to go to the location of the error or warning.
The following new features and changes apply to simulation settings and solvers:
MaxStep — Lets you specify the upper bound on solver step size for a deterministic solver. MaxStep is a property of the SolverOptions object.
Implicit Tau solver settings — For impltau, AbsoluteTolerance holds the value for convergence tolerance for the nonlinear solver that is used internally by the Implicit Tau solver. You can now specify AbsoluteTolerance for impltau. Previously, if you selected the Implicit Tau solver, the software ignored any changes to the AbsoluteTolerance and RelativeTolerance options within a configuration set and used the default values set internally.
UnitConversion — Supported by both deterministic solvers and stochastic solvers. Previously UnitConversion was supported only by the stochastic solvers.
The RelativeTolerance property is no longer valid for the Implicit Tau (impltau) solver.
When you load a file created in a previous version, the project loads the RelativeTolerance property. But when you save the file, the software updates the change.
The UnitConversion property default is now 'false'. If you load a SimBiology project created in a previous version into the SimBiology desktop, the UnitConversion setting in each model in the project remains as the saved setting. If however, you are running an M-file, you must now remember to set the UnitConversion property to true if you want the software to perform unit conversions
There are 14 new demos for SimBiology Version 2.0. Click SimBiology demos or type demo('MATLAB', 'SimBiology') at the command prompt.
| Version 2.0.1 (R2006b) SimBiology Software | Version 1.0.1 (R2006a) SimBiology Software | |
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