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 A-250 as indicated)
1300 York Avenue; 2nd Floor, Room C-200 (unless otherwise noted)
Midterm Exam: Thursday, November 3rd (5:30 pm – 7:00 pm) in Room A-250
Final Exam: Thursday, December 15th (5:30 pm – 7:00 pm) in Room C-200
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

1. Quantifying a Sample Distribution
   Tuesday, September 13th, 2016
   
   summary statistics, quantiles, SD vs. SEM, measurement variation vs. biological variation

2. 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

3. 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

4. Confidence Intervals and Contingency Tables
   Tuesday, September 27th, 2016
   This lecture will be held in Room A-250
   
   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
   Tuesday, October 4th, 2016
   
   duality between p-values and CIs, statistical vs. biological significance, choosing an appropriate α, type I and type II errors

6. Lab #2: Practical R (part II) (assignment due Thursday October 20th)
   Thursday, October 6th, 2016
   
   libraries and ggplot, producing publication quality plots, data driven graphics

7. 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 hard-to-obtain samples

8. Multiple Hypothesis Testing
   Tuesday, October 18th, 2016
   
   from Bonferroni to False Discovery Rate, dealing with non-normal data, t-tests re-visited

9. Lab #3: Optimal Stopping (due Thursday November 10)
   Thursday, October 20th, 2016
   
   the role of simulation in statistics, non-parametric tests, exploring the optimal stopping problem

10. Bayesian Methods
    Tuesday, October 25th, 2016
    
    how to incorporate prior knowledge into statistical models

11. Midterm Exam
    Thursday, November 3rd, 2016
    The midterm exam will be held in Room A-250

12. Election Day – No Class
    Thursday, November 8th, 2016

13. Correlation vs. Linear Regression (code | slides)
    Thursday, November 10th, 2016
    
    introduction to modeling in R; why $r^2$ is not the whole story

14. Principal Component Analysis (code | slides)
    Tuesday, November 15th, 2016
    
    data transformation and data reduction methods

15. Thanksgiving Break: No class
    Week of November 21st, 2016

16. Fitting Model Parameters to Data
    Tuesday, November 29th, 2016
    
    non-linear regression, a statistical view of curve fitting, confidence intervals revisited

17. Midterm Exam Review
    Thursday, December 1st, 2016

18. Quantitative Comparison of Models (lab)
    Tuesday, December 6th, 2016
    This lecture will be held in Room A-250
    
    how to avoid over-fitting, F-test and AICs, F-tests as a means of parameter estimation

19. Lab #4: Practical R (part IV)
    Thursday, December 8th, 2016
    Lab #4 will be held in Room A-250
    
    data wrangling with melt, dcast, and plyr

20. 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 LC-504
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

1. Introduction to Dynamic Systems and Linear Difference Equations (part I)
   Tuesday, January 26th, 2016

2. Introduction to Dynamic Systems and Linear Difference Equations (part II)
   Thursday, January 28th, 2016

3. Periodic Behavior and Complex Eigenvalues
   Tuesday, February 9th, 2016

4. A First Look at Eigenvectors
   Thursday, February 11th, 2016

5. Principal Component Analysis
   Tuesday, February 16th, 2016

6. Linear Difference Equations Laboratory
   Thursday, February 18th, 2016

7. Representing Time Dependent Phenomena with ODEs
   Tuesday, February 23rd, 2016

8. Stability and Linearization of ODEs (part I)
   Thursday, February 25th, 2016

9. Stability and Linearization of ODEs (part II)
   Lab 3 Due
   Tuesday, March 1st, 2016

10. Markov Chains and Hidden Markov Models & ODE Laboratory
    Thursday, March 3rd, 2016

11. Fourier Analysis and Signal Processing
    Lab 4 Due
    Tuesday, March 8th, 2016

12. FINAL EXAM (5:00 PM - 8:00 PM)
    Thursday, March 17th, 2016