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Build Models

Represent dynamics of mechanistic systems biology models, or PKPD systems

Functions

sbiomodel Construct model object
sbioroot Return SimBiology root object
sbioreset Delete all model objects
sbioselect Search for objects with specified constraints
sbiolastwarning SimBiology last warning message
sbiolasterror SimBiology last error message
addcompartment Create compartment object
addspecies Create species object and add to compartment object within model object
addparameter Create parameter object and add to model or kinetic law object
addreaction Create reaction object and add to model object
addrule Create rule object and add to model object
addevent Add event object to model object
findUnusedComponents Find unused species, parameters, and compartments in a model
findUsages(species,parameter,compartment) Find out how a species, parameter, or compartment is used in a model
findUsages(unit,unitprefix) Find out how a unit or unit prefix is used
findUsages(AbstractKineticLaw) Find out how an AbstractKineticLaw object is used
verify Validate and verify SimBiology model

Classes

Model object Model and component information
Compartment object Options for compartments
Species object Options for compartment species
Parameter object Parameter and scope information
Reaction object Options for model reactions
KineticLaw object Kinetic law information for reaction
Rule object Hold rule for species and parameters
Event object Store event information
Root object Hold models, unit libraries, and abstract kinetic law libraries
PKModelDesign object Helper object to construct pharmacokinetic model
PKCompartment object Used by PKModelDesign to create SimBiology model
PKModelMap object Define SimBiology model components' roles
construct Construct SimBiology model from PKModelDesign object
addCompartment Add compartment to PKModelDesign object

Examples and How To

Desktop Workflow

Create and Simulate a Simple Model

This example shows how to create and simulate a simple model of receptor-ligand kinetics using the SimBiology Desktop.

Programmatic Workflow

Construct a Simple Model

This example shows how to construct a one compartment model with two species, a parameter, and a reaction.

Fit a One-Compartment Model to an Individual's PK Profile

This example shows how to fit an individual's PK profile data to one-compartment model and estimate pharmacokinetic parameters.

Estimate Category-Specific PK Parameters for Multiple Individuals

This example shows how to estimate category-specific (such as young versus old, male versus female), individual-specific, and population-wide parameters using PK profile data from multiple individuals.

Concepts

What is a Model?

A SimBiology® model is a dynamic system described by a set of quantities and mathematical expressions.

Definitions and Evaluations of Rules

Rules are mathematical expressions that allow you to define or modify model quantities, namely compartment capacity, species amount, or parameter value.

Definitions and Evaluations of Reactions

A reaction is a mathematical expression that describe a transformation, transport, or binding process that changes one or more species.

Event Object

In SimBiology, an event is a discrete transition in value of a quantity or expression in a model.

Doses

Doses let you increase the amount of a species in a SimBiology model during simulation, either at specific time points or predefined time intervals.

Pharmacokinetic Modeling Functionality

SimBiology software extends the MATLAB® computing environment for analyzing pharmacokinetic (PK) data using models.

Create Pharmacokinetic Models

SimBiology lets you create one-, two-, or multi-compartment pharmacokinetic models for model simulation and parameter estimation.

Component Usage

SimBiology lets you find species, parameters, and compartments that are not used in a model and find out how they are used.

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