Schedule 2016
qBio I
Tuesday, September 13th, 2016 – Thursday, December 15th, 2016
Tuesdays and Thursdays, 5:30 PM – 7:00 PM
Location: Weill Auditorium (or A250 as indicated)
1300 York Avenue; 2nd Floor, Room C200 (unless otherwise noted)
Midterm Exam: Thursday, November 3rd (5:30 pm – 7:00 pm) in Room A250
Final Exam: Thursday, December 15th (5:30 pm – 7:00 pm) in Room C200
Course Directors:
 Jason Banfelder (jbanfelder@rockefeller.edu)
 Luce Skrabanek (las2017@med.cornell.edu)
 Michael LeVine (mil2037@med.cornell.edu)
Teaching Assistants (qbioi2016tas@gmail.com):
 Nimra Asi
 Gabriele Campanella
 Kevin Hadi
 Mehtap Isik
 Zijun Zhao
This course will be fully graded: (Honors, High Pass, Low Pass, Fail)
Class Sessions and Lecture Notes

Quantifying a Sample Distribution
Tuesday, September 13th, 2016
summary statistics, quantiles, SD vs. SEM, measurement variation vs. biological variation 
Probability Density Functions and the Normal Distribution (slides)
Tuesday, September 20th, 2016
binomial, Poisson, and normal distributions, testing for normality (part I): an introduction to formal statistical tests, testing for normality (part II): qqplots vs. formal tests 
Lab #1: Practical R (part I) (assignment due Tuesday October 4th)
Thursday, September 22nd, 2016
introduction to R, common data structures (vectors, factors, lists, dataframes), importing data 
Confidence Intervals and Contingency Tables
Tuesday, September 27th, 2016
This lecture will be held in Room A250
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
Tuesday, October 4th, 2016
duality between pvalues and CIs, statistical vs. biological significance, choosing an appropriate α, type I and type II errors 
Lab #2: Practical R (part II) (assignment due Thursday October 20th)
Thursday, October 6th, 2016
libraries andggplot
, producing publication quality plots, data driven graphics 
Statistical Power and Experimental Design
Tuesday, October 11th, 2016
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 
Multiple Hypothesis Testing
Tuesday, October 18th, 2016
from Bonferroni to False Discovery Rate, dealing with nonnormal data, ttests revisited 
Lab #3: Optimal Stopping (due Thursday November 10)
Thursday, October 20th, 2016
the role of simulation in statistics, nonparametric tests, exploring the optimal stopping problem 
Bayesian Methods
Tuesday, October 25th, 2016
how to incorporate prior knowledge into statistical models 
Midterm Exam
Thursday, November 3rd, 2016
The midterm exam will be held in Room A250 
Election Day – No Class
Thursday, November 8th, 2016 
Correlation vs. Linear Regression (code  slides)
Thursday, November 10th, 2016
introduction to modeling in R; why is not the whole story 
Principal Component Analysis (code  slides)
Tuesday, November 15th, 2016
data transformation and data reduction methods 
Thanksgiving Break: No class
Week of November 21st, 2016 
Fitting Model Parameters to Data
Tuesday, November 29th, 2016
nonlinear regression, a statistical view of curve fitting, confidence intervals revisited 
Midterm Exam Review
Thursday, December 1st, 2016 
Quantitative Comparison of Models (lab)
Tuesday, December 6th, 2016
This lecture will be held in Room A250
how to avoid overfitting, Ftest and AICs, Ftests as a means of parameter estimation 
Lab #4: Practical R (part IV)
Thursday, December 8th, 2016
Lab #4 will be held in Room A250
data wrangling withmelt
,dcast
, andplyr

Final Exam
Thursday, December 15th, 2016
qBio II
Tuesday, January 26th – Thursday, March 17th, 2016
Tuesdays & Thursdays, 5:00 PM – 6:30 PM
Location: Physiology Department Conference Room
1300 York Avenue; 5th Floor, Room LC504
Final Exam: Thursday, March 17th (5:00 PM – 8:00 PM)
Course Director: Jason Banfelder (jbanfelder@rockefeller.edu)
Teaching Assistant: Michael LeVine (mil2037@med.cornell.edu)
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, January 26th, 2016 
Introduction to Dynamic Systems and Linear Difference Equations (part II)
Thursday, January 28th, 2016 
Periodic Behavior and Complex Eigenvalues
Tuesday, February 9th, 2016 
A First Look at Eigenvectors
Thursday, February 11th, 2016 
Principal Component Analysis
Tuesday, February 16th, 2016 
Linear Difference Equations Laboratory
Thursday, February 18th, 2016 
Representing Time Dependent Phenomena with ODEs
Tuesday, February 23rd, 2016 
Stability and Linearization of ODEs (part I)
Thursday, February 25th, 2016 
Stability and Linearization of ODEs (part II)
Lab 3 Due
Tuesday, March 1st, 2016 
Markov Chains and Hidden Markov Models & ODE Laboratory
Thursday, March 3rd, 2016 
Fourier Analysis and Signal Processing
Lab 4 Due
Tuesday, March 8th, 2016 
FINAL EXAM (5:00 PM  8:00 PM)
Thursday, March 17th, 2016