|
|
|
| R2012a Documentation → SimBiology | |
Learn more about SimBiology |
|
| Contents | Index |
This table summarizes what's new in Version 3.4 (R2011a):
| New Features and Changes | Version Compatibility Considerations | Fixed Bugs and Known Problems |
|---|---|---|
| Yes Details below | Yes—Details labeled as Compatibility Considerations, below. See also Summary. | Bug
Reports Includes fixes |
New features and changes introduced in this version are:
The SimBiology desktop is redesigned to support:
Streamlined model-building workflow
Iterative workflows
Comparison of analysis results
The Project Explorer (outlined in red) is organized by Models, Tasks, and Data. After selecting a model, task, or data in the Project Explorer, then view and set related information in the Work Area (outlined in blue).
The desktop now lets you:
Use Full and Custom views for model building, in addition to the Table and Diagram views.
Create a task once, then run it on multiple models.
View and compare a summary of results from running like analysis tasks on one or more models.
Note Because the SimBiology desktop's more intuitive design better supports the model building and analyzing workflow, the context-sensitive help was removed from the desktop. |
SimBiology now supports arbitrary time units for simulation time, and is no longer limited to seconds. The default value of the TimeUnits property of a Configset object is second for a Model object created using sbiomodel, and hour for a Model object created from a PKModelDesign object. For details, see the TimeUnits property reference page.
Following is a new function:
| sbiofittool — Open SimBiology desktop for population fitting. |
There are improvements to the parameter estimation and population fitting features in SimBiology:
When performing a parameter estimation, you can now specify nonconstant parameter quantities (in addition to species amounts) to be matched during estimation. For details, see the description of observed_array in the sbioparamestim reference page.
When performing a parameter estimation, you can now specify compartment capacities and species amounts (in addition to parameter quantities) to be estimated. For details, see the description of estimated_array in the sbioparamestim reference page.
Some defaults for the method input for the sbioparamestim function have changed. Most defaults are the same as the defaults associated with the function selected as method. However, some defaults differ. For details, see the sbioparamestim reference page.
The defaults for the optionStruct input for the sbionlmefit and sbionlmefitsa functions have changed. The defaults for optionStruct are the same as the defaults for the name-value pair arguments accepted by the nlmefit and nlmefitsa functions, except:
The OptimFun argument's default is fminunc, if you have Optimization Toolbox™ installed. Otherwise, the default is still fminsearch.
The DerivStep field of the Options name-value pair argument. The default of the DerivStep field, when used by sbionlmefit or sbionlmefitsa, is the lesser of 1e-4, or the value of the SolverOptions.RelativeTolerance property of the configuration set associated with modelObj, with a minimum of eps^(1/3).
The default for the DerivStep field for the sbionlinfit function has changed. The default is now is the lesser of 1e-4, or the value of the SolverOptions.RelativeTolerance property of the configuration set associated with modelObj, with a minimum of eps^(1/3).
When using sbionlinfit to perform an individual fitting, if the fitting for an individual fails, the function returns a warning indicating the individual that failed, and then continues with the fitting, instead of returning an error and stopping.
In SimBiology Version 3.4, when using the following functions, the defaults of some input arguments have changed as explained above.
SimBiology now calculates individual weighted residuals, population weighted residuals, and conditional weighted residuals when performing population fitting.
Simulations of large models using SUNDIALS solvers now run faster.
When multiple events are triggered simultaneously, the event functions execute sequentially, in the order the events are listed in the model.
In SimBiology Version 3.3 and earlier, when multiple events were triggered simultaneously, each event function executed independently, at the same time, using the current state of the model. Then the results of the independently executed events merged in the order the events were listed in the model.
In SimBiology Version 3.4, when multiple events are triggered simultaneously, the event functions execute sequentially, in the order the events are listed in the model. This change impacts event functions that change model components in a dependent fashion. For details, see Evaluation of Simultaneous Events.
Following are new demos:
The Parameter Scanning, Parameter Estimation, and Sensitivity Analysis in the Yeast Heterotrimeric G Protein Cycle demo is updated to take advantage of some of the parameter estimation and population fitting enhancements.
 | Version 4.0 (R2011b) SimBiology Software | Version 3.3 (R2010b) SimBiology Software |  |
See how to analyze, visualize, and model biological data and systems using MathWorks products.
Get free kit| © 1984-2012- The MathWorks, Inc. - Site Help - Patents - Trademarks - Privacy Policy - Preventing Piracy - RSS |