Build Models

Represent dynamics of mechanistic systems biology models, or PKPD systems

Functions

`simbiology`	Open the SimBiology app to build PK/PD and mechanistic systems biology models
`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
`verify`	Validate and verify SimBiology model

`addcompartment`	Create compartment object
`addobservable`	Add observable object to SimBiology model
`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`	Find out how observable object is used in SimBiology model
`findUsages(unit,unitprefix)`	Find out how a unit or unit prefix is used
`findUsages(AbstractKineticLaw)`	Find out how an AbstractKineticLaw object is used
`updateInitialAssignments`	Update initial assignment rules to remove order dependencies

Classes

`Model object`	Model and component information
`Observable`	Object containing expression for post-simulation calculations
`Compartment object`	Object containing compartment information
`Species object`	Object containing species information
`Parameter object`	Parameter and scope information
`Reaction object`	Object containing model reaction information
`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

App Workflow

Create Model of Receptor-Ligand Kinetics

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

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.

Create and Simulate a Model with a Custom Function

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

Concepts

What is a SimBiology Model?

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

View Model Equations

You can view the system of equations that SimBiology creates when you build a model using reactions, rules, events, variants, and doses.

Species Object

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

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.

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.

Doses in SimBiology Models

Use doses to model different dosing regimens.

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, compartments, and observables that are not used in a model and find out how they are used.

Evaluation of Model Component Names in Expressions

SimBiology follows some precedence rules when evaluating names in expressions.

SimBiology Documentation

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