Lectures and Readings
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:
Last modified: Oct 13, 2011
