SAAM II

The fastest and most accurate way to create models, simulate experiments and analyze data

What is SAAM II


SAAM II is a modeling, simulation, and analysis software package which supports the development and statistical calibration of compartmental models in biological, metabolic, and pharmaceutical systems.

Used worldwide by more than 7,000 pharmaceutical, biomedical and bioengineering professionals – with citations in over 2,000 scientific publications, SAAM II is a proven and powerful tool for research, development, and teaching.

Additionally, SAAM II’s GUI is easy to learn and easy to use. Thus – regardless of level of modeling expertise – users can define models, run simulations, and analyze results quickly.

Under the hood, SAAM II employs state-of-the-art numerical and statistical methods and algorithms. It is widely regarded as the most robust and accurate software package for solving systems of differential equations and for fitting model parameters to experimental data sets with specified (and flexible) error models.

Why use SAAM II


Models and simulations developed using SAAM II provide a link to your experimental data. And with such model-experiment linkages, you will develop a deeper understanding of the roles, kinetics, and relative importance of the various sub-systems of interest in your experiments (e.g., plasma, tissue, kidney, G-I track).

Additionally, you can use SAAM II to generate “simulated experimental data” to test hypotheses and further increase your understanding. Such knowledge is extremely valuable when evaluating the safety, efficacy, and limitations of various interventions during treatment R&D.

While SAAM II has been applied mainly in areas of PK/PD and metabolism, it is a general-purpose compartmental modeling and simulation tool. Thus, any dynamic system which can be modeled using a system of compartments, fluxes, exogenous inputs, sinks, delays, etc. is a candidate for study with SAAM II. Recently SAAM II was used to successfully model the dynamics of influenza transmission throughout the U.S. population during the winter flu season of 2012-13.

How to use SAAM II


The typical SAAM II workflow goes as follows:

  1. Construct a model of your system using SAAM II’s graphical model building tools
  2. Provide initial estimates of kinetic rate constants inherent to the model
  3. Define your experimental protocol using various inputs and sample points. SAAM II provides for quite flexible experimental and sampling protocols to whatever level of complexity is required by your experiments
  4. Import your experimental data and define associated experimental error model(s)
  5. Solve the system of ordinary differential equations defined by your compartmental model structure and fit the model parameters to your experimental data. This may be as simple as using a single set of experimental data or it may involve using batch processing tools in SAAM II for incorporating multiple experimental data sets (e.g., to incorporate different patients and/or different experimental protocols and/or different experimental error conditions)
  6. Analyze results using various tools provided in SAAM II: statistical quantities related to the fit, plots, sensitivity analyses
  7. Refine model and/or experimental protocol (e.g., to test hypothesis, to increase accuracy of model) as needed

Minimal Models


In conjunction with the SAAM II application, The Epsilon Group offers minimal models (and associated documentation) designed for application of SAAM II to specific problems in glucose-insulin metabolism, the so-called glucose-insulin minimal models.

With SAAM II and such models, clinicians and researchers can analyze data from Intravenous Glucose Tolerance Tests (IVGTT), Oral Glucose Tolerance Tests (OGTT), and Mixed-Meal Tolerance Tests (MTT) to obtain fundamental metabolic information including insulin sensitivities, glucose effectiveness, and beta-cell responsivities. Such analyses enable the quantitative understanding of the complex relationship among beta-cell function, hepatic insulin extraction, and insulin action.

Contact TEG to learn more.

Learn More


The Epsilon Group maintains several resources which provide information for SAAM II users – from novice to expert. Follow the links below to explore these resources.

FAQs provide details on numerous aspects of the SAAM II software: from basic information such as installation, licensing, and operation of SAAM II to advanced topics covering expert techniques for solving and fitting with SAAM II for various modeling/simulation scenarios.
Click here to explore SAAM II FAQs …

Basic Tutorials provide step-by-step exercises using the SAAM II software illustrating its most commonly used features – i.e., features which almost all SAAM II users will employ at some time for their modeling/simulation tasks.
Click here to explore SAAM II basic tutorials …

Advanced Tutorials provide step-by-step exercises using the SAAM II software illustrating more advanced features of the software. Such advanced features are typically needed when modeling complex experimental protocols.
Click here to explore SAAM II advanced tutorials …

Publications in which SAAM II was used for modeling experimental data from investigations in PK/PD, metabolic, and other dynamic systems. By studying how SAAM II was used in these types of modeling/simulation studies, you will get a much greater understanding of the power and utility of the SAAM II software (and, thus, be able to use it more effectively for your own modeling/simulation needs).
Click here to explore SAAM II publications …


“SAAM II is absolutely essential for my modeling activities. Its flexibility and ability to analyze data sets from multiple experiments with multiple input-output designs makes it an integral component of my modeling toolbox.”

Peter L. Bonate, PhD, Senior Director, Global Head Pharmacokinetics, Modeling, and Simulation; Global Clinical Pharmacology & Exploratory Development, Pharma Global Development