SAAM II Compartmental Features

Compartmental Modeling with SAAM II


  • 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
    • Exogenous inputs
    • Transfers
    • Losses
  • Modeling tools include the:
    • Select, Compartment, Delay, and Flux tools, and the Lock check box
  • 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

  • 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

  • Users can choose any of 3 differential equation integrators
  • 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, based on the Pade approximation of the matrix exponential