User manual THE MATHWORKS SIMBIOLOGY RELEASE NOTES

[. . . ] SimBiology® Release Notes How to Contact MathWorks Web Newsgroup www. mathworks. com/contact_TS. html Technical Support www. mathworks. com comp. soft-sys. matlab suggest@mathworks. com bugs@mathworks. com doc@mathworks. com service@mathworks. com info@mathworks. com Product enhancement suggestions Bug reports Documentation error reports Order status, license renewals, passcodes Sales, pricing, and general information 508-647-7000 (Phone) 508-647-7001 (Fax) The MathWorks, Inc. 3 Apple Hill Drive Natick, MA 01760-2098 For contact information about worldwide offices, see the MathWorks Web site. SimBiology® Release Notes © COPYRIGHT 2005­2010 by The MathWorks, Inc. The software described in this document is furnished under a license agreement. The software may be used or copied only under the terms of the license agreement. [. . . ] Models containing events do not support sensitivity analysis. Variants 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. 38 Version 2. 2 (R2007b+) SimBiology® Software Support for Analysis Tasks in the Desktop The SimBiologydesktop now supports adding and managing analysis tasks through the following features: · "Task Manager" on page 39 · "Sensitivity Analysis in the Desktop" on page 40 · "Scanning and Scanning with Sensitivities in the Desktop" on page 41 · "Ensemble Simulation Runs in the Desktop" on page 41 · "Conserved Cycle Calculations in the Desktop" on page 41 · "Create Custom Analysis Tasks" on page 42 · "Generate Reports for Projects" on page 42 Task Manager 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. 39 SimBiology® Release Notes 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 in the Desktop 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. 40 Version 2. 2 (R2007b+) SimBiology® Software 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. Scanning and Scanning with Sensitivities in the Desktop 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" on page 39. 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. Ensemble Simulation Runs in the Desktop 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. [. . . ] When you export a model to an SBML file, you might lose some of these features. · Submodels are not supported by SBML export. · The abstract kinetic law name and corresponding expression are not supported by SBML, but the associated reaction rate equation is exported to SBML. · The properties Tag, UserData, and Active are not supported by SBML export. Tips Naming SimBiology Variables · If you are using a species or parameter name that is not a valid MATLAB variable name, do the following: - Enclose the name in square brackets when writing a reaction rate equation or a rule. [. . . ]