Schedule 2020
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

Introduction to Dynamic Systems and Linear Difference Equations (part I)
Tuesday, October 20th, 2020 
Introduction to Dynamic Systems and Linear Difference Equations (part II)
Thursday, October 22nd, 2020 
Periodic Behavior and Complex Eigenvalues
Tuesday, October 27th, 2020 
A First Look at Eigenvectors
Thursday, October 29th, 2020 
NO CLASS: Election Day (Principal Component Analysis lecture postponed)
Tuesday, November 3rd, 2020 
Principal Component Analysis  Linear Difference Equations Laboratory
Thursday, November 5th, 2020 (6:15 PM  7:45 PM) 
Representing Time Dependent Phenomena with ODEs
Tuesday, November 10th, 2020 
Stability and Linearization of ODEs (part I)
Thursday, November 12th, 2020 
Stability and Linearization of ODEs (part II)  ODE Laboratory
Tuseday, November 17th, 2020 
No class  Lab 1 Due
Thursday, November 19th, 2020 
Thanksgiving Break: No class
Tuesday, November 24th, 2020
Thursday, November 26th, 2020 
Markov Chains and Hidden Markov Models
Tuesday, December 1st, 2020 
Fourier Analysis and Signal Processing  Lab 2 Due
Thursday, December 3rd, 2020 
No Class (exam week)
Tuesday, December 8th, 2020 
FINAL EXAM
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:
 Jason Banfelder (jbanfelder@rockefeller.edu)
 Luce Skrabanek (las2017@med.cornell.edu)
Teaching Assistant:
 Ariana Clerkin (arb4007@med.cornell.edu)
Office Hours:
 Mondays, 46pm
This course will be fully graded: (Honors, High Pass, Low Pass, Fail)
Class Sessions and Lecture Notes

Quantifying a Sample Distribution  Code
Tuesday, 8 September, 2020
summary statistics, SD vs. SEM, measurement variation vs. biological variation 
Probability Density Functions and the Normal Distribution  Code
Thursday, 10 September, 2020
(note time: 6:157:45)
binomial, Poisson, and normal distributions, testing for normality: an introduction to formal statistical tests, qqplots vs. formal tests 
R Happy Hour (optional)
Friday, 11 September, 2020 
Confidence Intervals and Contingency Tables  Code
Tuesday, 15 September, 2020
ttests, working with proportional data, why CIs are more informative than pvalues, study types (retrospective, prospective, and cross sectional), working with rare events 
pValues and Formal Statistical Testing  Code
Thursday, 17 September, 2020
duality between pvalues 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 
R Happy Hour (optional)
Friday, 18 September, 2020 
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 hardtoobtain samples 
Group project: the optimal stopping problem  Code
Thursday, 24 September, 2020 
Multiple Hypothesis Testing and Nonparametric Tests  Code
Tuesday, 29 September, 2020
from Bonferroni to False Discovery Rate, dealing with nonnormal data, ttests revisited 
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 
Correlation vs. Linear Regression  Code
Tuesday, 6 October, 2020
(note time: 6:157:45)
introduction to modeling in R; why is not the whole story 
Fitting Model Parameters to Data  Code
Thursday, 8 October, 2020
nonlinear regression, a statistical view of curve fitting, confidence intervals revisited 
Quantitative Comparison of Models and ANOVA  Code
Tuesday, 13 October, 2020
how to avoid overfitting, Ftest and AICs, Ftests as a means of parameter estimation
Problem Set #3 
Graphics with ggplot2  Rmd file
ablation.csv
Data wrangling with tidyverse  Code
Thursday, 15 October, 2020