Education & Training
Computational Systems
Biology and Dose Response
Modeling Workshop
September 22-26, 2008
Division of Computational Biology
With support from the Superfund Basic Research Program
at Michigan State University
and the Exxon-Mobil Foundation.
What you will learn:
- Current computational modeling techniques for the quantitative investigation of how biological systems respond to perturbations
at the cellular level - Common themes in signal transduction and gene regulatory networks that underlie systems-level cellular behaviors including homeostasis, adaptation, threshold response, binary cell fate decisions, and irreversible differentiation
- To use these techniques to develop computational models for understanding and predicting dose response behaviors of drugs and environmental agents
Download course files
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Day 1
- Computational Dose Response Modeling Background
- Response Motifs in Quantitative Cell Signaling and Dose Response
- Introduction to Berkeley Madonna® and Exercise on Response Motifs
Day 2
- Binary Decision-Making in Biological Systems
- Mitogen-Activated Protein Kinase (MAPK)-Mediated Ultrasensitivity and Bistability
- Exercise: A Bistable Gene Auto-regulation Model
- Exercise: MAPK Ultrasensitivity and Bistability-Modeling Zenopus Oocyte Maturation
Day 3
- Response Motifs - Repeating Components Controlling Biological Function
- Exercise: Creating Feed Forward Loops and Sequential Gene Activation
- The Eukaryotic Cell Cycle and Checkpoint Control
- Exercise: Modeling a Simple Cell Cycle Circuit and Checkpoint Control
Day 4
- Cellular Homeostasis, Adaptation and Steady-State Dose Response
- Oxidative/Electrophilic Stress Response
- Exercise: Negative Feedback and Homeostasis
Day 5
- Stochasticity in Gene Expression and its Implication for Dose Response
- Computational Biology, Dose Response Modeling and Risk Assessment
- Optional Exercise: Switching through Activation of Cellular Circuits and Biological Consequences
Workshop Participation
Total attendees: 35
Inside The Hamner Institutes: 14
Outside The Hamner Institutes: 21
EPA: 9
FDA: 5
CDC: 1
Industry: 4
Academia: 2Click on images below to open larger versions in new window.
Selected student comments:
Accessibility:
“For someone without a strong math background, I was able to follow and understand. Exercises really forced that.”
“Synthesis of current literature into a clearly-organized format comprehensible to a very mixed audience and presented with exceptional skill.”
“The course was well planned, and accessible to people with various backgrounds.”
“I think that the instructors did an excellent job presenting the complex materials to people with a wide range of background.”
Usefulness:
“Finally able to put meaning into those cell response data. And open my imagination on all the possibility to understand human biology.”
“Gave me an idea about where to start with respect to studying the literature and applying the techniques of systems biology to my research.”
General comments
“Material was interesting in itself, but the instructors also taught the material well and make it understandable.”
“The instructors are excellent in deconstructing a complex problem and passing message without oversimplifying.”
“You guys were obviously well-prepared and had a phenomenal grasp of the subject matter. Great job! “
“This was a remarkable job, especially for a first offering.”
“Well organized, very well presented”, “Great, useful, and timely information. Exercises were very helpful.”
“Lectures were very well laid out”
“Exercises were well thought out, and illustrative of concepts covered in lecture.”
“Sequential organization of material with progressive increase in complexity.”
