Lectures and Readings

NSF CMACS Workshop, January 4-January 24, 2012

Wednesday, January 4


Welcome (Nancy Griffeth)

The Joy of Computational Biology (Nancy Griffeth)

Introduction to Biology (Stephen Redenti)

Using Unix on Mac OS (Terri Grosso)


Thursday, January 5


An Introduction to Modeling Biochemical Signal Transduction (James Faeder)

Modeling (Nancy Griffeth)

Modeling the Frog Cell Cycle (Nancy Griffeth)


Friday, January 6


Sort (Terri Grosso)

  1. Instructions
  2. Items

Math for Biology - An Introduction (Terri Grosso)

Exercises: the differential equations for the Frog Cell Cycle (Nancy Griffeth)

Lunch for all workshop attendees



  1. Sible & Tyson, Math Modeling, Methods 41, 2007 - describes the use of the Frog Cell Cycle Model
  2. Novak & Tyson, Numerical Analysis, J. Cell Sci 106, 1993 - the paper where the model was originally proposed


Monday, January 9


RuleBender (Kai Zhao)


Wednesday, January 11


Stochastic Markov Processes and Bayesian Networks (Aron Wolinetz)

Unit conversions for stochastic simulations (Nancy Griffeth, from notes by Justin Hogg)


Thursday January 12


Simulation Algorithms (Kai Zhao)

Project Overview (Nancy Griffeth)

EGFR (Kai Zhao)

Friday January 13 - Thursday January 19



Friday January 20


Visitor Talk: Bud Mishra on "Darwin, Development and Dysplasia: Signalling Games that Cells Play"

Monday, January 23


Student Presentations

Tuesday, January 24


Visitor Talk: Ilya Nemenman, "Universality of completion time distributions in complex biological networks"