A 2-day Workshop at Ohio State
University
8:30 AM - 5:00 PM August 28-29,
1997
Times for breaks and lunch to be
determined at the workshop.
Organized and presented by Robert D. Phair, Ph.D. of
BioInformatics Services, Rockville, MD, U.S.A.
The workshop was planned in cooperation with the SAAM
Institute, Inc., Seattle, WA, U.S.A.
A Workshop Notebook will be provided for each registered workshop participant. The notebook will contain copies of all of Dr. Phair's slides as well as ample space for notetaking. Also included are the SAAM Institute's SAAM II Tutorials and a diskette (PC format) containing all the tutorial and workshop files.
SAAM II User Guides will be available during the workshop for each team of participants.
Complexity - computers as tools
Workshop objectives
A flow chart for the modeling process
Modeling skills - Day 1: Model formulation, Protocol
imposition, Simulation, Testing
Model formulation
Scientific diagrams, cartoons, and roadmaps
Hands-on session: Drawing your diagram
Conservation of Mass
A vital concept: Steady State
A common error in formulating equilibrium models
Rate Laws
How do I know tracer rate laws are linear?
What to do at your model's boundary
The SAAM II Workspace
Hands-on session: Converting diagrams to SAAM II models
Protocol imposition
Protocol timelines
Hands-on session: Linking data sets to models
The Sample Attributes Dialog
Hands-on session: Entering your protocol in SAAM II
The Change Conditions Dialog
The Exogenous Input Dialog
"Creating" multiple experiments
Simulation
Establishing a pre-stimulus steady state
What to do when your model won't even solve
Hands-on session: Formulating stable isotope models
Model Testing
The Modeler's Workbench
Tools you should always have at your fingertips
The SAAM II Solutions Facility
The Show/Values Facility
Hands-on session: What to put in the data window
Individualized Consultation on Your Current Projects
Hands-on session: Formulating your own model
Modeling skills - Day 2: Biological theory
creation, Fitting, Publishing, Experimental design
Biological Theory Creation
What do I do when my model doesn't fit?
Data Fitting
Philosophy and practice of least squares fitting
The power of constraints
The beauty of forcing functions
Invoking a Forcing function
Are the parameters identifiable?
Evaluating a Fit
The SAAM II Statistics Window
Hands-on session: The SAAM Institute Tutorial on Data Fitting
Knowledge extraction and Publishing
The Holmes approach: The features of your data
What goes where in your modeling manuscript?
Experimental Design
Hands-on session: SAAM Institute Tutorial on Simulating
Experiments
The Achilles' Heel of Kinetic Analysis
The Case of the Slow Precursor
Individual Questions and Consultation
Hands-on session: Testing Your Own Model
The Workshop in Review
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