Verify Models
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 Builder | Build QSP, PK/PD, and mechanistic systems biology models interactively |
| SimBiology Model Analyzer | Analyze QSP, PK/PD, and mechanistic systems biology models |
Functions
verify | Validate and verify SimBiology model |
getequations | Return system of equations for model object |
sbiolastwarning | SimBiology last warning message |
sbiolasterror | SimBiology last error message |
findUnusedComponents | Find unused species, parameters, and compartments in a model |
findUsages | Find 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 |
updateInitialAssignments | Update initial assignment rules to remove order dependencies |
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.
