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• Online Tutorials: SAAM II  |  Case Studies: SAAM II
  FAQ: SAAM II  |  FAQ: PopKinetics

Online Tutorials: SAAM II

Note: Software capable of displaying a PDF is required for viewing or printing the following tutorials. Adobe Reader is available free of charge from the Adobe Web site at http://www.adobe.com/products/acrobat/readstep2.html.

• Basic Tutorials [75K PDF*]
  • Introduction [94K PDF*]
  • Getting Started with Compartmental [1.2M PDF*]
  • Getting Started with Numerical [640K PDF*]
  • Working with Data [987K PDF*]
  • Using Experimental Inputs (Basic) [564K PDF*]
  • Using Parameters (Basic) [606K PDF*]
  • Using the Sample Tool [605K PDF*]
  • Using Plots [616K PDF*]
  • Report Writing [562K PDF*]
  • Using Tables [412K PDF*]
    
    Basic Tutorials Study and Data Files [34K ZIP]
• Advanced Tutorials [76K PDF*]
  • Introduction [91K PDF*]
  • Creating Conditionals [741K PDF*]
  • Working with Change Conditions [604K PDF*]
  • Using Delays [809K PDF*]
  • Using Experimental Inputs (Advanced) [593K PDF*]
  • Multiple Input-Output Experiments [498K PDF*]
  • Using Forcing Functions [513K PDF*]
  • Using Parameters (Advanced) [713K DF*]
  • Saving and Restoring Solutions [394K PDF*]
  • Simulating Data [569K PDF*]
    
    Advanced Tutorials Study and Data Files [43K ZIP]
• Case Studies
  • Metabolic Case Studies [30K MSWord]
    • Glucose Kinetics: Two-Compartment Model [695K PDF*]
    • Glucose Kinetics: Three-Compartment Model [502K PDF*]
    • IVGTT : minimal model of cold glucose kinetics [202K PDF*]
    • Low Density Lipoprotein (LDL) metabolism [364K PDF*]
    • Insulin effect on LDL metabolism – perturbation by TPN [292K PDF*]
    • Leucine incorporation into very low density lipoprotein (VLDL) [203K PDF*]
    • Dynamic Contrast-Enhanced MRI Analysis of Tumor Data [206K PDF*]
    • Data Files [5K ZIP]
  • Numerical Case Studies [26K MSWord]
    • Diazepam Metabolism in Vitro - Michaelis-Menten Kinetics [728K PDF*]
    • Michaelis-Menten Enzyme Kinetics with Data Replicates [270K PDF*]
    • Data Files [2K ZIP]
  • Pharmacokinetic Case Studies [34K MSWord]
    • Cadralazine kinetics [425K PDF*]
    • Epsilon aminocaproic Acid (EACA) Pharmacokinetics/-Pharmacodynamics [261K PDF*]
    • Gentamicin kinetics – a simulation case study [228K PDF*]
    • Hydromorphone kinetics [643K PDF*]
    • Inulin kinetics [618K PDF*]
    • N-Acetylprocainamide (NAPA) kinetics [287K PDF*]
    • Theophylline Kinetics Following a Short Intravenous Infusion [458K PDF*]
    • Oral Theophylline Kinetics [657K PDF*]
    • Data Files [3K ZIP]
  • In 2004, the SAAM Institute in collaboration with Dr. Ron Sawchuk at the University of Minnesota sponsored a workshop in pharmacokinetics. Dr. Sawchuk, a long-time SAAM II user, had developed a series of case studies which he used in his courses. Three of these he has kindly agreed to let us include in our series of case studies.
    
    Drug interaction between AZT and probenecid Case Study [248K PDF*]
    
    • Data Files [1K txt]
    Cephalosporine Kinetics in Chinchilla [302K PDF*]
    • Data Files [1K txt]
    Nonlinear elimination with Bayesian priors [286K PDF*]
    • Data Files [1K txt]

*Software capable of displaying a PDF is required for viewing or printing this document. Adobe Reader is available free of charge from the Adobe website at http://www.adobe.com/products/acrobat/readstep2.html

Frequently Asked Questions: SAAM II

• Learning SAAM II
  • What documentation is provided with SAAM II?
  • Are there any on-line tutorials for SAAM II?
• Running SAAM II
• How do I export Tables from Solve or Fit into other graphical applications?
• How can I change Plot Labels and the size of the Plot Symbol?
• Does SAAM II work on Windows 2000/XP Professional?
• Is there an upper limit on the number of compartments for SAAM II?
• Solving (Simulation)
  • How can I calculate the Area Under the Curve for a generic function?
  • How can I calculate the Area Under the Curve to infinity?
  • How can I solve a differential equation that cannot be written in compartmental form?
  • How can I solve a second-order differential equation?
  • How can I solve a compartmental model where the rate constants are time varying?
  • How can I calculate the integral of a compartmental mass?
  • How can I calculate the derivative of a compartmental mass?
  • How can I analyze an algebraic model in the Compartmental application?
  • How do I handle data and change conditions or inputs that occur simultaneously?
  • How can I use data to simulate a function?
  • How can I change the data weighting method within a data column?
• Fitting (Optimization)
  • When and how should I use Bayesian fitting?
  • How do I set initial conditions for a sum of exponentials?
  • How do I analyze multiple data sets?
  • How can I calculate Statistics if SAAM II hasn't converged?
  • How can I make the Area Under the Curve a fitted variable?
  • How is the objective function calculated?
  • What should I do when the covariance matrix is unreliable?
  • What is the difference between absolute and relative weighting?
  • What is the right model to use?
  • What are the AIC and BIC?
  • What should I do when the fit goes on forever?
  • How do I implement time-dependent conditionals?
  • What's the easiest way to specify covariates in study files?
  • How can I get smoother curves on my plots?
  • How can I use Solutions when developing a model?
• Known Bugs!
  • Change Condition bug
  • Forcing Function setup bug
  • SAAM II crashes if Fitting with Compute Log and Plot open

Frequently Asked Questions: PopKinetics

• Running PopKinetics
  • How do I export tables from PopKinetics into other graphical applications?
  • What SAAM II version do I need to run PopKinetics?
• Known Bugs!
  • Help System Bug

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