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 Builder	Build QSP, PK/PD, and mechanistic systems biology models interactively (Since R2020b)
SimBiology Model Analyzer	Analyze QSP, PK/PD, and mechanistic systems biology models

Functions

`sbiomodel`	Construct model object
`sbioroot`	Return SimBiology root object
`sbioreset`	Delete all model objects
`sbioselect`	Search for objects with specified constraints
`sbiodiff`	Compare SimBiology models and diagram information (Since R2022a)
`getComponents`	Get model components associated with SimBiology model comparison results (Since R2022a)
`visdiff`	Visualize SimBiology model comparison results (Since R2022a)
`addcompartment`	Create compartment object and add to model or compartment
`addCompartment`	Add compartment to `PKModelDesign` object
`addobservable`	Add observable object to SimBiology model (Since R2020a)
`addspecies`	Create species object and add to model or compartment
`addparameter`	Create parameter object and add to model or kinetic law object
`addreaction`	Create reaction object and add to model
`addrule`	Add rule object to model
`addevent`	Add event object to model object
`construct`	Construct SimBiology model from `PKModelDesign` object
`generateCode`	Generate MATLAB function to recreate SimBiology model (Since R2024a)

Objects

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Modeling Components

`Model`	Model and component information
`Observable`	Object containing expression for post-simulation calculations (Since R2020a)
`Compartment`	Object containing compartment information
`Species`	Object containing species information
`Parameter`	Parameter and scope information
`Reaction`	Object containing model reaction information
`KineticLaw`	Kinetic law information for reaction
`Rule`	Hold rule for species and parameters
`SimBiology.Event`	Store SimBiology event information
`Root`	Hold models, unit libraries, and abstract kinetic law libraries
`SimBiology.DiffResults`	Results of comparison between two SimBiology models and diagrams (Since R2022a)

PK Objects

`PKModelDesign object`	Helper object to construct pharmacokinetic model
`PKCompartment object`	Compartment used by `PKModelDesign` to create SimBiology model
`PKModelMap object`	Define SimBiology model components’ roles

Topics

Model Building

Create Model of Receptor-Ligand Kinetics
Create and simulate a simple receptor-ligand kinetics model using SimBiology apps.
Incorporate SGLT2 Inhibition into Physiologically Based Glucose-Insulin Model Using SimBiology Model Builder
Update a glucose-insulin model to integrate sodium-glucose co-transporter 2 (SGLT2) receptor inhibition by a hypothetical compound.
Construct a Simple Model
This example shows how to construct a simple model programmatically.
Compare SimBiology Models
Compare any two SimBiology models to find out the differences between them.
Merge SimBiology Models
Merge differences between two SimBiology Models.
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.
SimBiology Model Matching Policy
SimBiology uses certain criteria and rules to compare models.