Syllabus for Mol 410/510 Fall 2011
MOL 410/510 Home | Syllabus | Reading material | Homework & solutions | Notes for Presentations
Classes are Tue/Thu 3-4:20 pm in LTL 118.
Homeworks will generally be handed out on Thursdays, and will be due the next Thursday.
(Exception: the homework out on Thu-15-Nov will be due back on Nov-29.)
Computer lab will be held Wednesday evenings at 7:30 pm in LTL 118.
(Exception: no computer lab during Fall Break or on Wed-21-Nov, the day before Thanksgiving.)
| Date | Lecture | Lecturer | Biologically-related problems | Reading | Essential additional reading | Notes/handouts | |
|---|---|---|---|---|---|---|---|
| Thu 13-Sep | Introduction | NW and TG | What you should know before class | Non-graded homework 0 | gfunc.zip | ||||
| Tue 18-Sep | Linear algebra I: vector spaces and matrices | TG | Systems of genes; or molecules; or neurons | ELA chap2 4 6 Strang | Linear Algebra primer Rules for vectors and matrices Scan of lecture notes. |
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| Thu 20-Sep | Linear algebra II: Eigenvalues and eigenvectors | TG | Red Blood Cell Production | Using Linear Algebra in Biology Scan of lecture notes. |
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| Tue 25-Sep | PCA and SVD (principles) | NW | Analyzing microarrays | Wal03 | SVD notes | ||
| Thu 27-Sep | PCA and SVD (examples) | NW | and other large data sets | Real-life example: PCA and protein folding | Clustering notes | ||
| Tue 2-Oct | 1-D linear dynamical systems | TG | Bacterial population growth; electrical membrane potential of neurons | Strogatz, Chap. 2 | Scan of lecture notes. | ||
| Thu 4-Oct | 2-D linear dynamical systems | TG | Gene regulation, genetic switch | Strogatz, Chap. 5 | Scan of lecture notes. | ||
| Tue 9-Oct | Intro to non-linear dynamical systems | TG | Population growth | Strogatz, Chap. 3 | Scan of lecture notes. | ||
| Thu 11-Oct | Bifurcations, stable and unstable limit cycles | TG | Genetic switch; Predator-prey model; Oscillating chemical reactions | Strogatz, Chap. 8.1-8.3 | Scan of lecture notes. | ||
| Tue 16-Oct | Limit cycles 2 | NW | Metabolic oscillations | Strogatz, Chap. 7.1-7.3, 7.5 | Lecture notes Additional lecture notes |
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| Thu 18-Oct | Weakly non-linear oscillators | NW | Strogatz, Chap. 7.6 | Lecture notes | |||
| Tue 23-Oct | Excitable systems | NW | Neurons, competence in B. subtilis | FitzHugh paper (1961) | Lecture notes | ||
| Thu 25-Oct | Midterm | ||||||
| BREAK | |||||||
| Tue 6-Nov | Chaos | NW | Heart rhythms-chaos health | Strogatz, Chap. 9.2-9.5 | May76 | Lecture notes | |
| Thu 8-Nov | Probability I | NW | Genetics, Mutations | Lecture notes | |||
| Tue 13-Nov | Probability II | NW | Stochastic process in cells | Lecture notes | |||
| Thu 15-Nov | Bayes’ Theorem | NW | Inferring models from data | Lecture notes | |||
| Tue 20-Nov | Diffusion | NW | Biochemistry in the cell | PDE | Kie53 | Lecture notes | |
| Thu 22-Nov | TURKEYS | ||||||
| Tue 27-Nov | Pattern Formation I | TG | Pattern in physical systems | Maini’04 | Cross&Hohenberg’93 | Lecture notes | |
| Thu 29-Nov | Pattern Formation II | TG | Pattern in biological systems | Koch&Meinhardt’94 | |||
| Tue 4-Dec | Fourier Transforms | TG | Lecture notes | ||||
| Thu 6-Dec | Time series I | NW | Analyzing noisy data | Lecture notes | |||
| Tue 11-Dec | Time series II | NW | Data-based prediction | Strogatz, Chap. 11.0-11.5 | Lecture notes | ||
| Thu 13-Dec | Project Presentations | students | |||||
| TBA in January | FINAL Exam |