Mickey Atwal


Programming Boot Camp

August 26-27
  • Command line
    • Introduction to command line and sequence data analysis slides.
    • Unix primer for biologists: link.

  • Python
    • Python, IPython and scientific packages can be installed via Enthought Canopy.
    • Introduction to Python programming notebook.
    • Codecademy interactive online course: link.

  • Applications
    • Replication analysis IPython notebook.
    • Binding site analysis IPython notebook.

  • Scientific computing with Python


  • Problem Set 1

Quantitative Biology I

September - October
  • Problem Set 1
  • Problem Set 2
    • questions:
Lecture Lecturer Topic Links
1. Sep 21 Atwal Introduction slides pdf
Bionumbers site
2. Sep 22 Atwal Probability, Statistics and Biological Noise slides pdf
Luria Delbruck pdf
distributions notebook
3. Sep 23 Atwal Correlations and Information Theory slides pdf
Shannon pdf
entropy notebook
Information theory slides pdf
4. Sep 24 Kinney Statistical Biochemistry slides pdf
5. Oct 15 Atwal Experimental Design and Testing slides pdf
6. Oct 16 Atwal Markov Models and Evolution slides pdf
7. Oct 19
Krasnitz Phylogeny slides pdf
R code
8. Oct 20
Atwal Machine Learning 1 slides pdf
9. Oct 22
Atwal Machine Learning 2 slides pdf
PCA notebook
10. Oct 23
Atwal Population Genetics 1 slides pdf
11. Oct 26
Atwal Population Genetics 2 slides pdf
A Siepel Dynamic Programming
slides pdf
B Siepel Alignment
slides pdf
C Siepel Fast-Alignment
slides pdf
D Siepel Motifs
slides pdf

Quantitative Biology II

February - April
Tue/Thur 2-4pm (unless stated otherwise below). Samet Room (Koch building).

Nice texts on machine learning
  • "Pattern recognition and machine learning" by C. Bishop
  • "Information theory, inference and learning algorithms" by D. Mackay (also available free online)

Lecture Lecturer Topic Links
1. Feb 26 Siepel Hidden Markov Models slides
2. Mar 3 Siepel Expectation Maximization Algorithm slides
3. Mar 9 (2.30pm) Siepel Markov Chain Monte Carlo slides
4. Mar 10 Atwal Variational Methods slides
5. Mar 12 Koulakov Independent Component Analysis Matlab files
6. Mar 17 Koulakov Support Vector Machines Matlab files
7. Mar 19 Koulakov Reinforcement Learning Matlab files
8. Mar 24 Kinney Gaussians and Laplace Approximation
9. Mar 26 Kinney Diagrammatic Methods
10. Mar 31 Kinney Density Estimation
11. Apr 2 Kinney Survival Analysis
12. Apr 7 Atwal Model Complexity coin tossing notebook
13. Apr 9 Atwal Ising Models Hopfield network paper
bistable perception paper
neural interaction paper
14. Apr 14 Atwal Biological Information Processing