SAAM II Compartmental Application

• Fast Setup for model and experiment building (point and click):

  • No programming or pseudo code,

  • Easy construction of complex models and complex experimental protocols,

  • Generates systems of equations automatically from the model structure; users can define additional equations.

• Flexible input capability includes bolus, constant infusion, primed infusion and equation.

• Forcing functions are easily inserted as user-defined or associated with data.

• Change conditions can be easily defined.

• User can choose any of 3 differential equation integrators

Easy construction of complex models and complex experimental protocols

• The Model pane Toolbox used to build models consisting of:

  • Compartments,

  • Delays,

  • Endogenous inputs,

  • Transfers, or

  • Losses.

• Modeling tools include the:

  • Select, Compartment, Delay, and Flux tools, and the Lock check box.

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• The Experiment tools create, modify, or delete an experiment. 

• The Experiment button activates the experiment tools and displays the current experiment. 

• The Select tool deactivates any previously chosen tool and  selects or moves experiment objects on the drawing canvas. 

• The Sample tool is used to create new samples.

Generates systems of equations automatically from the model structure; Users can define additional equations

• The Equations Defined Elsewhere pane contains a list of the equations implied by the graphical objects and configuration, and those written elsewhere in object attribute boxes. 

• The Equations Defined Here pane contains a list of additional equations used to further define other model variables.

Flexible input capability includes bolus, constant infusion, primed infusion and equation

• The Exogenous Input window is used  to enter the type, quantity, and duration of inputs into one or more compartments.

• There are four types of inputs which can be explicitly defined or automatically repeated at regular intervals.

Forcing functions are easily inserted as user-defined or associated with data

• Use of Forcing Functions allows a complex model to be broken into segments by forcing the contents of a compartment to simulate the output of another part of the model. 

• The Forcing Function can be defined by an equation or by linearly interpolated data. 

• In the Experiment mode the notation FF will show in a compartment containing a Forcing Function.

Change conditions can be easily defined

• Users can choose any of 3 differential equation integrators

• The Change Conditions window provides a means to change the value of a variable during the course of an experiment.

• At the time the user  specifies a Change Condition, the integrator stops and the change takes effect. 

• The change can either be instantaneous or continuous from a specified start time to a specified stop time.

SAAM II provides a choice of three integration methods

• The Rosenbrock integrator uses a semi-implicit method (default).

• The Runge-Kutta integrator uses a standard forward integrating order 5-4 method.

• The Pade integrator uses a method developed by the Resource Facility for Kinetic Analysis at the University of Washington; it is based on the Pade approximation of the matrix exponential.  The Integrator pane is shown to the right

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SAAM II Numerical Application  I  Other Features

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