Main Content

Verify Models

Verify SimBiology models and underlying mathematical expressions

Examine the model structure, validity of mathematical expressions, and consistency of units and dimensions using model verification tools. View the underlying model equations and check the initial conditions in the apps or at the command line.

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

verifyValidate and verify SimBiology model
getequationsReturn system of equations for model object
sbiolastwarningSimBiology last warning message
sbiolasterrorSimBiology last error message
findUnusedComponentsFind unused species, parameters, and compartments in a model
findUsagesFind out how a species, parameter, or compartment is used in a model
getadjacencymatrix (model)Get adjacency matrix from model object
getstoichmatrix (model)Get stoichiometry matrix from model object

Topics

Model Verification

SimBiology® has functionality that helps you find and fix warnings that you might need to be aware of, and errors that would prevent you from simulating and analyzing your model.

Evaluation of Model Component Names in Expressions

SimBiology follows some precedence rules when evaluating names in expressions.

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.

Determining the Adjacency Matrix for a Model

An adjacency matrix is a square matrix that provides information on reactants and products of reactions in a model.

Determining the Stoichiometry Matrix for a Model

A stoichiometry matrix provides stoichiometric information about reactants and products in model reactions.