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Libraries

The SimBiology® libraries are collections of built-in components that you can use to build and analyze models. For instance, you can use built-in units such as mole or molecule as amount units for species. As you perform model analyses, you can use built-in plots such as box plot or residuals plot to display the analysis results. You can also add custom components to any library. For instance, you can define a custom unit or block and use it as you build models. Similar to preferences, libraries are saved across sessions of MATLAB® and the SimBiology desktop. Libraries are available for all projects and are not part of any one project. You can also export libraries and share with others by selecting Export All Libraries from the action menu.

To open a library in the SimBiology desktop, select Content > Libraries and double-click a library. For instance, the following figure shows the kinetic laws library with all the available built-in kinetic laws.

Kinetic Laws Library

As you configure model reactions, you can use predefined reaction rates that follow particular kinetics such as mass action or Michaelis-Menten. SimBiology provides a list of such predefined rates in the Kinetic Laws library.

The kinetic law for a newly added reaction is configured to MassAction by default, and SimBiology automatically creates and maps the species and parameters needed by the reaction rate. For other kinetic laws, only parameters are created and mapped. You need to create and map the species manually. For details about configuring reaction rates in the SimBiology desktop, see View by Expressions. Use the Unknown kinetic law to define a custom reaction rate with its own parameters. You must define and add the species and parameters needed by the custom rate.

Note

The MassAction and Unknown kinetic laws can have different simulation results even when the reaction rate is the same. This can happen when you have a reversible reaction with species in different compartments. The difference in simulation results is because of the volume-scaling performed by SimBiology during the dimensional analysis. For details, see Deriving ODEs from Reactions. Specifically, for MassAction, SimBiology uses corresponding compartment volumes to multiply the forward and reverse rates. However, for Unknown and other built-in kinetic laws, SimBiology multiplies the entire rate by only one compartment which contains the reactants. To see exactly what compartment volumes are used for scaling, open the Equations View and check the ODEs section.

Units Library

It provides a collection of units that you can use. The library displays the unit composition for each unit. The Menu Display column controls how each unit is displayed when selecting quantity units in the Table or Diagram views. For instance, suppose you have a custom unit with the unit composition mole/(liter*second). Depending on what you select in the Menu Display, SimBiology displays it differently in the Units column of Table Overview.

Unit Prefixes Library

It provides a list of all the available unit prefixes.

Blocks Library

It contains blocks that you can use to build models interactively. SimBiology provides a default block library called ModelBuilding that contains built-in blocks representing all modeling elements. In addition to built-in blocks, you can create custom blocks with different appearances. For instance, you can customize a receptor protein to have a different block shape or color than other species. You can use these blocks to build a model graphically in the diagram view. For details about different built-in block types, see Built-in Blocks.

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