• SimBiology Overview

• Integrating SimBiology Models into Your Existing Workflow

  Using the SimBiology Desktop vs. the Command Line

• SimBiology and SBML

• SimBiology Desktop Overview

• Understanding SimBiology Projects and Libraries

• Managing SimBiology Projects and Libraries

• About The Gene Regulation Model

  Creating a SimBiology Model

  Adding the Reaction for Transcription

  Adding the Reaction for Translation

  Adding the Reactions for Gene Regulation

  Adding the Reactions for mRNA and Protein Degradation

• Simulating the Model

• Simulating the Model with a Stochastic Solver

  More Examples of Using the Command Line

• What is a Model?

• Model Modifiers

• Representing a Model and Model Modifiers in SimBiology

• Example - Creating A Model That Changes a Species Amount Using an Event

• Example - Creating A Model That Changes a Parameter Value Using a Variant

• Example - Creating A Model That Uses a User-Defined Function in an Expression

  Overview of Structural Analysis

• Verifying a Model

  Example - Verifying a Model

• Determining Conserved Moieties

  Example - Determining Conserved Moieties

• Determining the Adjacency Matrix for a Model

• Determining the Stoichiometry Matrix for a Model

• Overview of Simulation and Analysis

• Simulating Models

• Example - Simulating a Model and Viewing Results

• Calculating Sensitivities

• Example - Calculating Sensitivities

• Estimating Parameters

• Example - Estimating Parameters Using sbioparamestim

• Accelerating Model Simulations and Analyses

• Pharmacokinetic Modeling Functionality

• Importing Data - Supported Files and Data Types

• Importing Data

• Creating Pharmacokinetic Models

• Parameter Fitting in Pharmacokinetic Models

• Fitting Pharmacokinetic Model Parameters

• Defining Reaction Rates with Mass Action Kinetics

• Defining Reaction Rates with Enzyme Kinetics

  Using Rate Rules When the Rate of Change Is Constant

  Using Rate Rules When the Rate of Change Is Exponential

  Using Rate Rules When the Rate of Change Is Determined by Another Species

  Using Rate Rules To Express Differential Rate Equations as Rules

• Minimal Cascade Model for a Mitotic Oscillator

• Model of the Yeast Heterotrimeric G Protein Cycle

• Model of M-Phase Control in Xenopus Oocyte Extracts

  Objects

  Abstract Kinetic Laws

  Compartments

  Configuration Sets

  Covariate Analysis

  Events

  Kinetic Laws

  Models

  Parameters

  Pharmacokinetic Modeling

  PKCovariate Analysis

  Reactions

  RepeatDose

  Root

  Rules

  ScheduleDose

  SimData

  Species

  Units and Unit Prefixes

  Variants

• Using Object Methods

  Abstract Kinetic Law

  Compartments

  Configuration Sets

  CovariateModel

  Events

  Kinetic Laws

  Models

  NMFileDef

  Parameters

  PKCompartment

  PKData

  PKCovariateModel

  PKModelDesign

  PKModelMap

  Reactions

  RepeatDose

  Root

  Rules

  ScheduleDose

  SimData

  Species

  Unit

  Unit Prefix

  Variant

• Using Object Properties