NSF-CMACS Workshop -- Winter 2010
I. | Introduction | ||
Additional Reading: | |||
Systems Biology Q and A from Nature | |||
A. | The life cycle of a cell | ||
B. | Mac OS X and Unix | ||
An index of bash commands | |||
C. | The role of signaling in the cell's life cycle | ||
D. | Discussion slides for modeling | ||
E. | Modeling Biochemical Systems | ||
F. | Chemical kinetics | ||
G. | Exercise: Modeling a toy signaling pathway | ||
II. | Visiting lecture by Jim Faeder: Using Modeling to Bridge Scales in Biology | ||
III. | Wiring Diagrams | ||
IV. | A normal signaling pathway: the unreplicated DNA checkpoint (G2 to M) | ||
A. | Exercise: | ||
B. | Additional Reading: | ||
V. | Model checking to understand signaling pathways that lead to cancer | ||
A. | Temporal Logic | ||
B. | Model Checking | ||
C. | Extending the model of the EGFR signaling pathway | ||
Reading: A Model of the Epidermal Growth Factor Receptor (EGFR) Pathway |
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D. | Experiments with the EGFR signaling pathway |
Glossaries: