Build Models

Represent dynamics of mechanistic systems biology models, or PKPD systems

Functions

simbiologyOpen the SimBiology app to build PK/PD and mechanistic systems biology models
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

Classes

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

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, and compartments 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.