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)
Math for Biology - An Introduction (Terri Grosso)
Exercises: the differential equations for the Frog Cell Cycle (Nancy Griffeth)
Lunch for all workshop attendees
Reading:
- Sible & Tyson, Math Modeling, Methods 41, 2007 - describes the use of the Frog Cell Cycle Model
- 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
Project
Friday January 20
Visitor Talk: Bud Mishra on "Darwin, Development and Dysplasia: Signalling Games that Cells Play"
Monday, January 23
Tuesday, January 24
Visitor Talk: Ilya Nemenman, "Universality of completion time distributions in complex biological networks"