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

  D. Experiments with the EGFR signaling pathway


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