Main Content

Build Models

Build mechanistic systems biology models or PK/PD models

Build QSP, PBPK, PK/PD, and systems biology models graphically using a block diagram editor or programmatically using MATLAB® functions. Use doses to model various dosing regimens and use variants to represent biological variability and what-if scenarios.

Apps

SimBiology Model BuilderBuild QSP, PK/PD, and mechanistic systems biology models interactively
SimBiology Model AnalyzerAnalyze QSP, PK/PD, and mechanistic systems biology models

Functions

sbiomodelConstruct model object
sbiorootReturn SimBiology root object
sbioresetDelete all model objects
sbioselectSearch for objects with specified constraints
addcompartmentCreate compartment object
addCompartmentAdd compartment to PKModelDesign object
addobservableAdd observable object to SimBiology model
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
constructConstruct SimBiology model from PKModelDesign object

Objects

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ModelModel and component information
ObservableObject containing expression for post-simulation calculations
CompartmentObject containing compartment information
SpeciesObject containing species information
ParameterParameter and scope information
ReactionObject containing model reaction information
KineticLawKinetic law information for reaction
RuleHold rule for species and parameters
EventStore event information
RootHold 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

Topics

Model Building

Create Model of Receptor-Ligand Kinetics

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

Incorporate SGLT2 Inhibition into Physiologically Based Glucose-Insulin Model Using SimBiology Model Builder

Incorporate sodium-glucose co-transporter 2 (SGLT2) receptor inhibition by a hypothetical compound into an existing glucose-insulin model.

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.

Create and Simulate a Model with a Custom Function

This example shows how to create a custom function and incorporate it in model simulation.

Define Reaction Rates with Mass Action Kinetics

Use mass action kinetics to define zero-order, first-order, second-order, and reversible reactions.

Define Reaction Rates with Enzyme Kinetics

Use differential equations, mass action kinetics, or Michaelis-Menten kinetics to define enzyme reactions.

Events in SimBiology Models

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

Create Pharmacokinetic Models

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

Model Definitions

What is a SimBiology Model?

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

Species Object

A species object represents a species, which is the amount of a chemical or entity that participates in reactions.

Doses in SimBiology Models

Use doses to model different dosing regimens.

Variants in SimBiology Models

Use variants to store alternate parameter values and initial conditions of a model.

Definitions and Evaluations of Rules in SimBiology Models

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 in SimBiology Models

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