SimBiology

Analyzing Models

You can use SimBiology to perform sensitivity analysis, parameter sweeps, and Monte Carlo simulations to investigate the influence of model parameters and initial conditions on model behavior. You can visualize the change in model dynamics when a parameter or initial condition is varied over a prespecified range. Alternatively, you can sample values from a distribution to incorporate a known uncertainty in parameter values into model evaluation. SimBiology also provides a forward sensitivity analysis task to calculate local, time-dependent sensitivities to parameter values and initial conditions.

Figure 5: Outputs from parameter scan and sensitivity analysis tasks. Live Plots in the Task Editor showing the effect of drug clearance rate on the time-concentration profile and drug exposure and sensitivity of receptor dynamics to model parameters.
Figure 5: Output plots for parameter scan and sensitivity analysis tasks. Live plots in the Task Editor show the effect of drug clearance rate on the time-concentration profile and drug exposure (left) and the sensitivity of receptor dynamics to model parameters (right).

Interactive Exploration Tools

SimBiology provides exploration tools that let you vary parameter values, initial conditions, and dose schedules with sliders. The interactive tools enable you to quickly iterate through values without modifying the base model. When you move a slider, you can instantaneously visualize the outcome of that change on the task results.

The exploration section for each task can be independently configured to ask different questions. For example, you could configure one task to examine the effect of binding and unbinding constants on fractional receptor occupancy, and you could set up another task for the same model to iterate through dose amounts and intervals to achieve a target exposure level.

Figure 6: Explorer section in the Task Editor configured to inspect the effect of parameters and dosing schedules on the tumor growth profile.
Figure 6: Explorer section in the Task Editor configured to inspect the effect of parameters and dosing schedules on the tumor growth profile.

Custom Analysis

SimBiology provides MATLAB functions to programmatically simulate and analyze your models. These programmatic tools enable you to develop custom analyses, automate workflows, and integrate SimBiology models into other MATLAB applications. For example, you could use constrained optimization algorithms from Optimization Toolbox and Global Optimization Toolbox to identify dosing strategies that maximize tumor suppression while satisfying constraints imposed by safety considerations.

Figure 7: Custom optimization algorithm to identify infusion rate required to achieve a target peak concentration for an influential protein in the signaling pathway.
Figure 7: Custom optimization algorithm to identify the infusion rate required to achieve a target peak concentration for an influential protein in the signaling pathway.
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Biologia dei Sistemi e Modellazione Farmacocinetica con SimBiology

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