• SimBiology Model Components

• Defining Reaction Rates with Mass Action Kinetics

• Defining Reaction Rates with Enzyme Kinetics

• Evaluation of Reaction Rate

• Using Constant Amount and Boundary Condition for Species

• Scoping Parameters for Reactions, Rules, and Events

• Changing Model Component Values Using Rules

• Changing Model Component Values Using Events

• Desktop Example - Changing Species Amounts Using an Event

• Storing and Applying Alternate Model Values Using Variants

• Desktop Example - Applying Changes to Parameter Value Using a Variant

• Verifying that a Model Has No Warnings or Errors

• Desktop Example - Using User-Defined Functions in Expressions

• Importing and Exporting Model Component Data

• Performing Simulations

• About Simulation Solvers

• Nonstiff Deterministic Solvers

• Stiff Deterministic Solvers

• Stochastic Solvers

  Sundials Solvers

• Accelerating Simulations

• Scanning Analysis

• Desktop Example - Scanning

• Sensitivity Analysis

• Desktop Example - Calculating Sensitivities

• Command-Line Example - Calculating Sensitivities

• Parameter Estimation

• Command-Line Example - Parameter Estimation

• Moiety Conservation

• Command-Line Examples - Determining Conserved Moieties

• Desktop Example - Creating Custom Analysis

• Visualizing Results Using Plot Types

• Desktop Example - Creating and Using Plot Types

• Pharmacokinetic Modeling Functionality

• Importing Data - Supported Files and Data Types

• Importing Data at the Command Line

• Importing Data into the SimBiology Desktop

• Working with Imported Data and the SimBiology Desktop

• Creating Pharmacokinetic Models

• Parameter Fitting in Pharmacokinetic Models

• Fitting Pharmacokinetic Model Parameters at the Command Line

• Fitting Pharmacokinetic Model Parameters in the SimBiology Desktop

• Goldbeter Model

• SimBiology Model with Rate Rules

• SimBiology Model with Reactions

  References

  Objectives

• Background on G Protein Cycles

• Modeling a G Protein Cycle

• Building the G Protein Cycle Model

• Completing the SimBiology Model

• Simulating the G Protein Cycle Model

• Creating the Mutant Strain Using a Variant

• Creating a Custom Plot-Type to View Simulation Results

• Plotting Species from Two Different Data Sets

• Plotting Experimental Data with Simulation Data

  References

• M-Phase Control Model

• M-Phase Control Equations

• SimBiology Model with Rate and Algebraic Rules

• SimBiology Model with Reactions and Algebraic Rules

  References

  Objects

  Abstract Kinetic Laws

  Compartments

  Configuration Sets

  Events

  Kinetic Laws

  Models

  Parameters

  Pharmacokinetic Modeling

  Reactions

  RepeatDose

  Root

  Rules

  ScheduleDose

  SimData

  Species

  Units and Unit Prefixes

  Variants

• Using Object Methods

  Abstract Kinetic Law

  Compartments

  Configuration Sets

  Events

  Kinetic Laws

  Models

  NMFileDef

  Parameters

  PKCompartment

  PKData

  PKModelDesign

  PKModelMap

  Reactions

  RepeatDose

  Root

  Rules

  ScheduleDose

  SimData

  Species

  Unit

  Unit Prefix

  Variant

• Using Object Properties