SimBiology

Building Models

SimBiology lets you represent a model of a biological or a pharmacological mechanism just as you would draw it on a piece of paper. It includes a block diagram editor that lets you graphically build models by dragging and connecting blocks. You can also programmatically build and manage models using MATLAB functions.

In addition to the environment for building models, SimBiology includes a library of standard PK models. Or, you can import models from a Systems Biology Markup Language (SBML) file.

Building a Model in SimBiology 12:56
Build and simulate a model using the SimBiology desktop.

Building Blocks

SimBiology provides three basic blocks to build your models:

  • Species represent dynamic states of the model, typically the concentration or amount of an entity, such as a drug, protein, gene, or metabolite.
  • Compartments represent physically isolated regions in which you can associate sets of species.
  • Reactions represent interactions between one or more species, such as transformation, transport, and binding processes.
Figure 1: Diagram view of a Drug-Receptor binding model that includes 3 species, 2 reactions, and 1 compartment.
Figure 1: Diagram view of a drug-receptor binding model that includes three species (blue rectangles), two reactions (red circles), and one compartment (black rectangle). The Species Drug and Receptor are binding to form the Complex species, which is being degraded via the Complex Degradation reaction.

Specifying Model Dynamics

SimBiology uses a reaction-network modeling approach that lets you model a variety of dynamic biological systems such as signaling pathways, metabolic networks, and the pharmacokinetics/pharmacodynamics of drugs. Each reaction in the model defines the structure and the rate of the individual interaction. SimBiology uses mass-balance principles to automatically translate this network representation of the model into a set of ordinary differential equations (ODEs) that mathematically describe the dynamics of your system.

The equation view displays the underlying ODEs defining the model.

Figure 2: Diagram view of a Drug-Receptor binding model. Equation view showing the equations describing the model dynamics.
Figure 2: Diagram view (left) of a drug-receptor binding model, with equation view (right) showing the equations describing the model dynamics.

SimBiology provides two additional modeling constructs for specifying model dynamics:

  • Rules define relationships or dependencies between model quantities that cannot be represented as a reaction. For example, you can use a rule to define fractional receptor occupancy as a function of free receptor and bound receptor concentrations.
  • Events define a sudden, discrete change in model behavior based on a specified condition. For example, you can use an event to reset a parameter value at a certain time point or when a certain concentration threshold is crossed.

Taken together, model expressions—that is, reactions, rules, and events—fully describe the mathematics of the model.

Model Variants

Model variants let you store a set of parameter values or initial conditions that are different from the base model configuration. Using variants, you can easily simulate alternate scenarios and what-if hypotheses without creating multiple copies of the model. For example, you can use model variants to specify parameter values for different cell lines, drug candidates, or animal species.

Model Doses

SimBiology allows you to define and evaluate bolus and infusion dosing strategies. You can link the dose to the appropriate species in the model to stipulate the administration route (intravenous, subcutaneous, oral, or topical). You can test hybrid dosing strategies by including multiple dosing schedules during model evaluation. Similarly, you can assess the benefit of combination therapies and determine the optimal dosing strategy by combining dosing schedules targeting different model species.

Next: Simulating Models

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