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This table summarizes what's new in Version 2.2 (R2007b+):
| 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 following new features and changes apply to a model's structure:
SimBiology models now let you add compartments to a model, specify compartment size, simulate, and do analysis with multiple compartments. Any model containing species must have a compartment, and the species must belong to a compartment. You can also perform dimensional analysis and unit conversion accounting for the specified compartment size. For more information on compartments, refer to the following sources in the documentation:
Compartment — Introduction to compartments in the SimBiology Getting Started Guide.
Compartment object — Reference for compartment objects.
Support for submodels will be removed in a future release. You can still open models containing submodels and create submodels, but you cannot simulate or perform any analysis tasks on the model. Therefore, you should transition to using compartments where applicable.
Compatibility Considerations. If you have submodels in your previously created model, you can still open your model, but you must convert the submodels into top-level SimBiology models to be able to perform any tasks.
To convert submodels, use sbioupdate.
If you open a model that contains submodels in the SimBiologydesktop, the submodels are automatically converted to models and placed in separate model sessions. See sbioupdate for more information.
As a result of removing submodels, the addmodel method and Models property of the model object are no longer relevant. You can still access the addmodel method and the Models property for this version of the software, though it may be removed in a future release.
You can now add events to SimBiology models. Use events to describe sudden changes in a model system. Events are supported only by the sundials solver and the stochastic solver ssa.
For more information on events, refer to the following:
Events — Introduction to events in the SimBiology Getting Started Guide.
Changing Model Component Values Using Events — Discussion about events including how events are evaluated in the SimBiology User's Guide.
Event object — Reference for event objects.
Sundials Solvers — Deterministic solver for simulating models with events in the SimBiology User's Guide.
Models containing events do not support sensitivity analysis.
Variants let you store the names and values of model components and use the values stored in a variant as the alternate value to apply during a simulation. You can store values for species InitialAmount, parameter Value, and compartment Capacity in a variant.
For more information on variants, refer to the following:
Variants — Introduction to variants in the SimBiology Getting Started Guide.
Variant object — Reference for variant objects in the SimBiology Reference.
Desktop Example — Applying Changes to Parameter Value Using a Variant — Example in a tutorial in the SimBiology Model Reference.
In the SimBiology desktop, expand Model Variable Settings and double-click Variants to open the Variants pane. The SimBiology Desktop Help updates with more information on adding and setting variants. If the help is not open in the desktop, select Help > SimBiology Desktop Help.
The SimBiologydesktop now supports adding and managing analysis tasks through the following features:
The Task Manager lets you add and manage simulation and analysis tasks. In the Project Explorer, double-click Model Session. The Model Session pane opens with the Task Manager listed on the right.
Click a task to add it to your model. The desktop adds the task to the Project Explorer and opens the task pane. For more information on setting up and running a task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help.
Sensitivity analysis is now supported in the desktop. Sensitivity analysis was previously available only through command line. Sensitivity analysis lets you calculate the time-dependent sensitivities of a species specified in SpeciesOutputs with respect to species initial conditions and parameter values.
See Performing Sensitivity Analysis Using the Desktop in the SimBiology User's Guide for more information. You must have a model in the desktop for this feature to be enabled.
For more information on sensitivity analysis, see Sensitivity Analysis in the SimBiology User's Guide.
You can perform species and parameter scanning analysis alone or in combination with sensitivity analysis in the desktop. Scan a parameter value or a species initial amount to determine the effect of a range of values of the parameter or species.
Combine the scan with sensitivity analysis to explore the sensitivity of a species with respect to a range of values of a parameter or a species.
For information on how to add the task to a model, see Task Manager. For more information on setting up and running the task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help. You need a model in the desktop for this feature to be enabled.
The SimBiologydesktop now supports ensemble simulations. You can perform ensemble simulations using the stochastic solvers to gather data from multiple stochastic runs of the model.
See Running Ensemble Simulations in the Desktop in the SimBiology User's Guide for more information. You need a model in the desktop for this feature to be enabled.
The SimBiologydesktop now supports conserved cycle calculations. This feature lets you calculate a complete set of linear conservation relations for the species in a SimBiology model object. For an introduction, see Moiety Conservation in the SimBiology User's Guide.
For information on how to add the task to a model, see Task Manager. For more information on setting up and running the task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help. You need a model in the desktop for this feature to be enabled.
The SimBiologydesktop lets you create custom tasks that are associated with a project. You can either write new code or copy and modify task code from built-in tasks in the desktop. For more information about creating custom tasks, see Desktop Example — Creating Custom Analysis in the SimBiology User's Guide.
For information on how to add the task to a model, see Task Manager. For more information on setting up and running the task in the desktop, open the task pane and select Help > SimBiology Desktop Help to see the context-sensitive help. You need a model in the desktop for this feature to be enabled.
You can now generate reports for your projects. Report templates let you generate a report with specified information about a model. To generate a template, in the Project Explorer, click Report Templates to open the Report Templates pane. Select Help > SimBiology Desktop Help to see the context-sensitive help for information on how to generate reports.
Built-in and user-defined libraries for units, unit prefixes, and abstract kinetic laws are now organized under two root object properties, BuiltInLibrary and UserDefinedLibrary, with subcategories for units, unit prefixes, and abstract kinetic laws. See Root object, BuiltInLibrary, and UserDefinedLibrary in SimBiology Reference for more information.
In previous versions, the libraries were organized under six properties:
UserDefinedKineticLaws
BuiltInKineticLaws
UserDefinedUnits
BuiltInUnits
UserDefinedUnitPrefixes
BuiltInUnitPrefixes
The changes to the library structure improve the organization of root object properties.
To illustrate the change using an example, previously you would access a user-defined kinetic law using the following syntax:
rootObj = sbioroot; get(rootObj, 'UserDefinedKineticLaws')
You must now use the following syntax:
rootObj = sbioroot; get(rootObj.UserDefinedLibrary, 'KineticLaws')
The following new features and changes apply to solvers and simulation settings:
The Sundials package of solvers has been added in this release. The Sundials solvers are part of a freely available third-party package developed at Lawrence Livermore National Laboratory. Models that contain events are supported by the Sundials solvers and by the stochastic solver ssa. For more information, see Sundials Solvers in the SimBiology User's Guide.
The new property DefaultSpeciesDimension lets you specify whether the default species dimensions should be concentration (default) or substance. This property thus lets you specify whether the solver should account for compartment capacity. If however, you specify the species units in the InitialAmountUnits property, these units define the species dimension regardless of the value in DefaultSpeciesDimension.
The SimBiology SimData object now stores the data returned from any simulation. For example, the output from the sbiosimulate function is now stored in a SimData object which holds time and state data as well as metadata, such as the types and names for the logged states or the configuration set used during simulation.
You can also store data from multiple simulation runs as an array of SimData objects. Thus, the output of sbioensemblerun is an array of SimData objects. See SimData object for more information and a list of methods and properties.
Compatibility Considerations. The SimData object is now the preferred container for simulation and analysis task data. Previously, simulation and analysis data were stored as time series objects. Functions that used to return time series objects now return SimData objects. If you have time series objects in your projects, you can convert them using sbioupdate. Functions that used to take a time series object as an input argument now take SimData object. You can use time series objects in an input argument, but you see a warning. Support for time series objects in SimBiology functions may be removed in a future version.
The sbiogetsensmatrix and sbiogetnamedstate functions are being replaced by the SimData object methods getsensmatrix and selectbyname respectively.
There are two new plot functions — sbioplot and sbiosubplot. Both functions let you plot data directly from the SimData object (see SimData Object Holds All Simulation Data).
sbioplot plots each simulation run for a SimData object or array of SimData objects from a model in the same figure. The plot is a time plot of each state in the object. The figure also shows a hierarchical display of all the runs in a tree, where you can choose which trajectories to show.
sbiosubplot plots each simulation run for a SimData object or array of objects into its own subplot. The subplot is a time plot of each state in the object. You can navigate through the plots in the figure window and select a subset of the plots to view.
To set up sensitivity analysis, you must now specify an additional property called SpeciesOutputs. In SpeciesOutputs, specify the species for which you want to compute sensitivities.
Previously, sensitivity analysis used the species specified in StatesToLog as the species for which sensitivities should be calculated. SpeciesOutputs improves the functionality by separating the use of the properties.
If you have models from a previous version configured for sensitivity analysis, you must specify species for which you want to compute sensitivities in the SpeciesOutputs property. Until this property is specified, sensitivity analysis gives a warning that the SpeciesOutputs property is not set, and continues to use the species specified in StatesToLog. The use of StatesToLog in this context may not be available in a future version, so you should set the SpeciesOutputs property for your models, if applicable.
Units and unit prefixes are now represented by objects. You can create units and prefixes and add them to the user-defined library using the function sbioaddtolibrary. See Unit object and UnitPrefix object for more information.
Previously, sbioregisterunit and sbiounregisterunit created and removed units respectively. These functions now produce warnings and will be removed in a future version. Use unit objects and sbioremovefromlibrary instead.
Similarly, sbioregisterunitprefix and sbiounregisterunitprefix created and removed unit prefixes respectively. These functions now produce warnings and will be removed in a future version. Use unit prefix objects and sbioremovefromlibrary instead.
For more information about the process of removing functions, see "About Functions Being Removed" in What Is in the Release Notes.
 | Version 2.3 (R2008a) SimBiology Software | Version 2.1.2 (R2007b) SimBiology Software |  |
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