SimBiology® 2.3

Product Description

• Introduction and Key Features
• Working with SimBiology®
• Building a Model
• Running a Simulation
• Analyzing a Model
• Saving and Exporting Results

Analyzing a Model

SimBiology provides functionality that lets you gain insight into your model via parameter estimation, sensitivity analysis, and conservation of moieties.

Parameter Estimation

With SimBiology you can calibrate the response of your model to experimental data, eliminating the need to tune model parameters by trial and error or to develop your own optimization routines. You can estimate parameters with MATLAB or by using optimization algorithms in Optimization Toolbox™ (available separately).

Sensitivity Analysis

SimBiology lets you calculate the sensitivities of all system species relative to the specified parameters and species initial conditions. This analysis helps you better understand the behavior of the network and lets you determine parameters of highest importance. Sensitivities to various initial conditions allow investigation into the behavior of the network across populations.

SimBiology provides several options for analyzing sensitivities. These include the following:

• Computed sensitivities can be normalized or presented without normalization.
• Sensitivities can be computed relative to a user-specified set of parameters, species initial conditions, or both.

Moieties Conservation

You can find and analyze the conserved moieties, or quantities, in your model to gain insight into the model's structure and function. SimBiology provides three algorithms to determine conserved moieties: QR factorization, row-reduction, and semi-positive (taken from convex analysis and optimization). You can specify the following output views for your conserved moieties:

• Graphical view with conserved moieties highlighted in the block diagram editor
• A conservation matrix accompanied by a cell array containing species names
• A readable format of conservation relations
• A link matrix that relates dependent and independent species

Parameter estimation (left) and sensitivity analysis (far left) are examples of analysis functionality provided by SimBiology®. Click on image to see enlarged view.