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Simulate Responses to Biological Variability

Simulate biological variability to compare animal species, strains, mutants, or experimental conditions

Functions

sbiovariant Construct variant object
addvariant Add variant to model
sbiosimulate Simulate SimBiology model
sbiosteadystate Find steady state of SimBiology model
sbioaccelerate Prepare model object for accelerated simulations
sbiosampleparameters Generate parameters by sampling covariate model (requires Statistics and Machine Learning Toolbox software)
sbiosampleerror Sample error based on error model and add noise to simulation data
createSimFunction Create SimFunction object
sbioplot Plot simulation results in one figure
sbiosubplot Plot simulation results in subplots
sbiotrellis Plot data or simulation results in trellis plot
sbioensemblerun Multiple stochastic ensemble runs of SimBiology model
sbioensembleplot Show results of ensemble run using 2-D or 3-D plots
sbioensemblestats Get statistics from ensemble run data

Classes

SimData object Simulation data storage
Configset object Solver settings information for model simulation
SolverOptions Specify model solver options
RuntimeOptions Options for logged species
CompileOptions Dimensional analysis and unit conversion options
SimFunction object Function-like interface to execute SimBiology models
SimFunctionSensitivity object SimFunctionSensitivity object, subclass of SimFunction object

Examples and How To

Construct a Simple Model

This example shows you how to construct a simple model with two species (A and B) and a reaction.

Simulate the Yeast Heterotrimeric G Protein Cycle

This example shows how to configure simulation settings, add an event to the model to trigger a time-based change, save, and plot the simulation results.

Simulate Biological Variability of the Yeast G Protein Cycle Using the Wild-Type and Mutant Strains

This example shows how to create and apply a variant to the G protein model of a wild-type strain.

Concepts

Model Simulation

SimBiology lets you simulate the dynamic behavior of a model.

Model Modifiers

SimBiology lets you use doses and variants to modify and perturb a model from its base configuration.

Choosing a Simulation Solver

SimBiology® uses a solver function to compute solutions for a system of differential equations at different time intervals during model simulation.

SUNDIALS Solvers

SUNDIALS is an advanced computational package for solving systems of nonlinear algebraic equations, ODE, or DAE systems.

Stochastic Solvers

The stochastic simulation algorithms provide a practical method for simulating reactions that are stochastic in nature.

Accelerating Model Simulations and Analyses

You can accelerate the simulation or analysis by converting the model to compiled C code.

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