Quantitative Understanding in Biology
Spring 2008

Home | Schedule and Lecture Notes | Prerequisites | Grading

Module I: Statistics

11-Feb: Quantifying a Sample Distribution (lecture notes)
13-Feb: Probability Density Functions and the Normal Distribution (lecture notes)
18-Feb: (President’s Day Holiday)
20-Feb: Confidence Intervals and Contingency Tables (lecture notes)
25-Feb: P-Values and Formal Statistical Tests (lecture notes)
27-Feb: Closing Thoughts and Review (lecture notes)
3-Mar: Statistics Computer Laboratory

Module II: Model Parameter Estimation

5-Mar: Correlation and Linear Regression (lecture notes)
10-Mar: Fitting Model Parameters to Data: Part I
12-Mar: Fitting Model Parameters to Data: Part II (lecture notes)
17-Mar: Quantitative Comparison of Models (lecture notes)
19-Mar: Parameter Estimation Computer Laboratory (problem set)
24-Mar: Models of Visual Neuron Function -- Dr. Daniel Butts (presentation)

Module III: Linear Difference Equations and Linear Algebra

26-Mar: Introduction to Linear Difference Equations I (lecture notes)
31-Mar: Introduction to Linear Difference Equations II (lecture notes -- same as above)
2-Apr: Linear Algebra Review
2-Apr: Bayesian Statistics -- You are welcome to attend this lecture (part of the Bioinformatics couse) held 1:30 - 4:30 PM in LC-504.
7-Apr: Analysis of Systems of Linear Difference Equations
9-Apr: No class
14-Apr: Linear Difference Equations Computer Laboratory (problem set)
16-Apr: SPECIAL TOPICS LECTURE: Applications of Markov Chains to Ion Channels (Dr. Colleen Clancy)
21-Apr: (Spring Break Holiday) 23-Apr: (Spring Break Holiday)

Module IV: Ordinary Differential Equations

28-Apr: Midterm exam -- The exam will be given in the Physiology conference room, LC-504 (1300 York Ave).
30-Apr: Representing Time Dependent Phenomena with ODEs; Numerical Evaluation of ODE Models (lecture notes)
5-May: Analysis of Sets of Linear ODEs (lecture notes)
7-May: Non-linear ODEs and Stability (lecture notes -- same as above; link to pplane7)
12-May: ODE Computer Lab (problem set)
14-May: SPECIAL TOPICS LECTURE: Introduction to Control Theory (Dr. Emre Aksay)
19-May: SPECIAL TOPICS LECTURE: Voltage Gated Channels (Dr. Colleen Clancy)
21-May: Fourier Analysis (lecture notes)
26-May: (Memorial Day Holiday)

Module V: Partial Differential Equations

28-May: Representing Spatially Dependent Phenomena with PDEs (Uche Kannu)
2-Jun: SPECIAL TOPICS LECTURE: Medical Image Analysis (Dr. Bryan Kressler) (scripts: celldemo.m, graddemo.m, invfilt.m)
4-Jun: Divergence, Gradient, and Curl (lecture notes)
9-Jun: Student's Final Project Presentations (Huang and Kherlopian) / PDE Computer Lab (problem set)
11-Jun: Student's Final Project Presentations (Chachra and Segota; Wang and Mu)

Conclusion

16-Jun: Class Canelled
18-Jun: Student’s Final Project Presentations (Sylvester et. al.; Lianoglou)-- This lecture will meet in the ICB conference room (Y13.01) from 10:00 to 11:30 AM
18-Jun: SPECIAL TOPICS LECTURE: Network Modeling (Dr. Emre Askay) -- This lecture will meet in LC-504 from 1:30 PM to 4:30 PM
23-Jun: Student’s Final Project Presentations (Tschetter; Feldman)
25-Jun: Student’s Final Project Presentations (Rizwan; Coward)
30-Jun: Final Exam -- The exam will be given in the Physiology conference room, LC-504 (1300 York Ave).