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Version 3.0 (R2009a) SimBiology Software

This table summarizes what's new in Version 3.0 (R2009a):

New Features and Changes	Version Compatibility Considerations	Fixed Bugs and Known Problems	Related Documentation at Web Site
Yes Details below	No	Bug Reports Includes fixes	No

New features and changes introduced in this version are:

• New Feature to Import, Visualize, and Statistically Analyze Clinical and Experimental Data

• New Functionality to Create Pharmacokinetic Models

• New Functionality to Fit Data and Estimate Parameters Using Nonlinear Mixed Effects

• New Diagnostic Plots for Individual and Population Fitting Results

• New Project Wizard to Add Data, Create Models, and Specify Tasks

• New simbiology Command to Open the SimBiology Desktop

• Enhanced Usability Features in the SimBiology Desktop

• New Demo for Pharmacokinetic Modeling

New Feature to Import, Visualize, and Statistically Analyze Clinical and Experimental Data

You can import tabular data into the SimBiology desktop or the MATLAB Workspace. The supported file types are .xls, .csv, and .txt.

At the command line, you can process and visualize the data using command-line functions. In the SimBiology desktop, you can filter the raw data to suppress outliers, visualize data using MATLAB plots, and calculate statistics to analyze the data. You can further choose to plot the imported data with any analysis task.

See Importing Data in the SimBiology User's Guide for more information.

New Functionality to Create Pharmacokinetic Models

You can automatically generate pharmacokinetic (PK) models by specifying number of compartments, dosing type, and method of elimination. If you plan to use the MATLAB command line, see Creating PK Models at the Command Line in the SimBiology User's Guide for more information.

If you plan to use the SimBiology desktop, the new Add Model wizard lets you automatically generate PK models in the desktop. See Creating PK Models in the SimBiology Desktop Using a Wizard in the SimBiology User's Guide for more information.

In addition, in the SimBiology desktop you can start by creating a new project using the new Project Wizard which also lets you add data, create models, and add analysis tasks in a SimBiology project. See New Project Wizard to Add Data, Create Models, and Specify Tasks for additional information.

New Functionality to Fit Data and Estimate Parameters Using Nonlinear Mixed Effects

You can perform both individual and population fits to grouped longitudinal data.

• Individual fit — Fit data using nonlinear least squares method, estimate parameters, and calculate residuals and the estimated coefficient covariance matrix.

• Population fit — Estimate the fixed effects and the random sources of variation on parameters, using nonlinear mixed-effects models.

  You can use two classes of methods to approximate the likelihood of the model:

  • Methods that directly estimate parameters using the likelihood function namely, LME and RelME.

  • Methods that linearize the likelihood function, namely, first-order approximation (FO) and first-order approximation at the conditional estimates ('FOCE').

For more information, see Parameter Fitting in Pharmacokinetic Models in the SimBiology User's Guide.

New Diagnostic Plots for Individual and Population Fitting Results

In the SimBiology desktop, after fitting the data, the analysis generates diagnostic plots that show:

• The predicted time courses and observations for an individual or the population

• Observed versus predicted values

• Residuals versus time, group, or predictions

• Distribution of the residuals

• A box-plot for random effects or parameter estimates from individual fitting.

For more information, see Visualizing Parameter Fitting Results and Generating Diagnostic Plots in the SimBiology User's Guide.

New Project Wizard to Add Data, Create Models, and Specify Tasks

The newly added Project Wizard in the SimBiology desktop lets you:

• Add data from text files, spreadsheets, or the MATLAB Workspace.

• Create models, including automatically generate pharmacokinetic models by specifying number of compartments, dosing type, and method of elimination.

• Specify analysis tasks to add to the project.

For an example of how to use the Project Wizard, see Modeling Using the SimBiology Graphical User Interface in the SimBiology Getting Started Guide.

New simbiology Command to Open the SimBiology Desktop

A new function, simbiology, has been added for enhanced usability in opening the SimBiology desktop. simbiology is equivalent to the sbiodesktop function, which is also supported.

Enhanced Usability Features in the SimBiology Desktop

The following enhancements to the SimBiology desktop are included in this release:

• Back and Forward buttons to help with navigation between desktop panes

• In Preferences, the ability to choose default model tasks to add to a model when loading an SBML file or importing a model from the MATLAB Workspace

New Demo for Pharmacokinetic Modeling

There is a new demo showing pharmacokinetic modeling functionality (Modeling the Population Pharmacokinetics of Phenobarbital in Neonates). To see all demos, click SimBiology demos or type demo('MATLAB', 'SimBiology') at the command prompt.

Version 3.1 (R2009b) SimBiology Software

Version 2.4 (R2008b) SimBiology Software

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