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Modeling Workflow

A SimBiology® model is a dynamic system described by a set of quantities and mathematical expressions. There are three types of quantities: species, parameter, and compartment. Three types of expressions describe the mathematical relationships among quantities. The first type of expression is a reaction which describes a process such as a transformation, transport, binding or unbinding of reactants and products. Another type of expression is a class of assignment equations (rules) which define how quantity values are initialized or updated. The third type is an event that describes a change in a quantity value during simulation. For details about SimBiology models, see What is a Model?.

Biological variability can be modeled using a modeling element called variant. A variant is a collection of quantities with alternate values. Variants do not change the original quantity values permanently. For instance, you can have a set of values for immunological parameters of a healthy person represented by a variant and a different set of values for a cancer patient represented by another variant. You can then simulate the model with each variant to see the predictions for both cases.

An increase in a species amount or concentration due to an external stimulus such as an oral or intravenous administration of a drug can be modeled using an element called dose. You can use an array of doses to explore different dosing regimens and determine the optimal dosing strategy. For details, see Doses.

A model can be built and visualized in three different views: the Diagram view, Table view, and Equations view. Each view is a different representation of the same model. For example, the Diagram view shows a graphical representation of the model and lets you build models interactively. For details on all views, see Model Views.

As you build a model, the desktop checks if there are any errors or warnings and identifies them using message indicators. You can hover over each indicator to see the corresponding warning or error message. During model verification, the desktop examines many aspects of the model including the model structure and validity of mathematical expressions. It also verifies the consistency of units and dimensions, and flags any issues.

You can save multiple models in one project, which uses a native file format ending in *.sbproj. Alternatively, a model can be saved to an SBML–formatted file, but some SimBiology features not supported by SBML are not saved with the model. For details, see SBML Support.

Given a model, you can perform several model analyses such as simulation, parameter estimation, and sensitivity calculation. For details, see Analysis Workflow.

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