qBio II

Tuesday, October 20th, 2020 – Thursday, December 10th, 2020
Tuesdays & Thursdays, 5:30 PM – 7:30 PM
Location: Zoom
Course Director: Derek Shore (des2037@med.cornell.edu)
Course Director: Jason Banfelder (jbanfelder@rockefeller.edu)
Office Hours: Mondays, 4:00 PM - 5:00 PM
This course will be fully graded: (Honors, High Pass, Low Pass, Fail)

Class Sessions and Lecture Notes

  1. Introduction to Dynamic Systems and Linear Difference Equations (part I)
    Tuesday, October 20th, 2020

  2. Introduction to Dynamic Systems and Linear Difference Equations (part II)
    Thursday, October 22nd, 2020

  3. Periodic Behavior and Complex Eigenvalues
    Tuesday, October 27th, 2020

  4. A First Look at Eigenvectors
    Thursday, October 29th, 2020

  5. NO CLASS: Election Day (Principal Component Analysis lecture postponed)
    Tuesday, November 3rd, 2020

  6. Principal Component Analysis | Linear Difference Equations Laboratory
    Thursday, November 5th, 2020 (6:15 PM - 7:45 PM)

  7. Representing Time Dependent Phenomena with ODEs
    Tuesday, November 10th, 2020

  8. Stability and Linearization of ODEs (part I)
    Thursday, November 12th, 2020

  9. Stability and Linearization of ODEs (part II) | ODE Laboratory
    Tuseday, November 17th, 2020

  10. No class | Lab 1 Due
    Thursday, November 19th, 2020

  11. Thanksgiving Break: No class
    Tuesday, November 24th, 2020
    Thursday, November 26th, 2020

  12. Markov Chains and Hidden Markov Models
    Tuesday, December 1st, 2020

  13. Fourier Analysis and Signal Processing | Lab 2 Due
    Thursday, December 3rd, 2020

  14. No Class (exam week)
    Tuesday, December 8th, 2020

    Thursday, December 10th, 2020

qBio I

Tuesday, September 8th, 2020 – Tuesday, October 15th, 2020
Tuesdays and Thursdays, 5:30 PM – 7:00 PM (except where noted)
Location: Zoom

Course Directors:

Teaching Assistant:

Office Hours:

  • Mondays, 4-6pm

This course will be fully graded: (Honors, High Pass, Low Pass, Fail)

Class Sessions and Lecture Notes

  1. Quantifying a Sample Distribution | Code
    Tuesday, 8 September, 2020

    summary statistics, SD vs. SEM, measurement variation vs. biological variation

  2. Probability Density Functions and the Normal Distribution | Code
    Thursday, 10 September, 2020
    (note time: 6:15-7:45)

    binomial, Poisson, and normal distributions, testing for normality: an introduction to formal statistical tests, qqplots vs. formal tests

  3. R Happy Hour (optional)
    Friday, 11 September, 2020

  4. Confidence Intervals and Contingency Tables | Code
    Tuesday, 15 September, 2020

    t-tests, working with proportional data, why CIs are more informative than p-values, study types (retrospective, prospective, and cross sectional), working with rare events

  5. p-Values and Formal Statistical Testing | Code
    Thursday, 17 September, 2020

    duality between p-values and CIs, statistical vs. biological significance, choosing an appropriate α, type I and type II errors

    Problem Set #1: Understanding Type I error rates
    R Markdown | Rmd file | HTML file
    Intro to R | Code

  6. R Happy Hour (optional)
    Friday, 18 September, 2020

  7. Statistical Power and Experimental Design | Code
    Tuesday, 22 September, 2020

    why you cannot just add a few N to your dataset when p > 0.05, appreciating the economics (in time and money) of experimental design, statistical vs. biological significance revisited, designing experiments around hard-to-obtain samples

  8. Group project: the optimal stopping problem | Code
    Thursday, 24 September, 2020

  9. Multiple Hypothesis Testing and Non-parametric Tests | Code
    Tuesday, 29 September, 2020

    from Bonferroni to False Discovery Rate, dealing with non-normal data, t-tests re-visited

  10. Bayesian Methods
    Unbiased Coin example | Fair Coin example 1 | Fair Coin example 2 | Unfair Coin example
    Thursday, 1 October, 2020

    how to incorporate prior knowledge into statistical models

  11. Correlation vs. Linear Regression | Code
    Tuesday, 6 October, 2020
    (note time: 6:15-7:45)

    introduction to modeling in R; why is not the whole story

  12. Fitting Model Parameters to Data | Code
    Thursday, 8 October, 2020

    non-linear regression, a statistical view of curve fitting, confidence intervals revisited

  13. Quantitative Comparison of Models and ANOVA | Code
    Tuesday, 13 October, 2020

    how to avoid over-fitting, F-test and AICs, F-tests as a means of parameter estimation

    Problem Set #3

  14. Graphics with ggplot2 | Rmd file
    Data wrangling with tidyverse | Code
    Thursday, 15 October, 2020