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Build Models

Represent dynamics of mechanistic systems biology models, or PKPD systems


sbiomodelConstruct model object
sbiorootReturn SimBiology root object
sbioresetDelete all model objects
sbioselectSearch for objects with specified constraints
sbiolastwarningSimBiology last warning message
sbiolasterrorSimBiology last error message
verifyValidate and verify SimBiology model
addcompartmentCreate compartment object
addspeciesCreate species object and add to compartment object within model object
addparameterCreate parameter object and add to model or kinetic law object
addreactionCreate reaction object and add to model object
addruleCreate rule object and add to model object
addeventAdd event object to model object
findUnusedComponentsFind 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
updateInitialAssignmentsUpdate initial assignment rules to remove order dependencies


Model objectModel and component information
Compartment objectOptions for compartments
Species objectOptions for compartment species
Parameter objectParameter and scope information
Reaction objectOptions for model reactions
KineticLaw objectKinetic law information for reaction
Rule objectHold rule for species and parameters
Event objectStore event information
Root objectHold models, unit libraries, and abstract kinetic law libraries
PKModelDesign objectHelper object to construct pharmacokinetic model
PKCompartment objectUsed by PKModelDesign to create SimBiology model
PKModelMap objectDefine SimBiology model components’ roles
constructConstruct SimBiology model from PKModelDesign object
addCompartmentAdd 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 simple model programmatically.

Model a Gene-Regulation Pathway

This example shows how to construct a simple gene-regulation model and simulate it.


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.


Use doses to model different dosing regimens.

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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