[ qBio I | qBio II ]

qBio I

Tuesday, September 1st, 2015 – Thursday, October 29th, 2015
Tuesdays and Thursdays, 5:00 PM – 6:30 PM
Location: Weill Auditorium
1300 York Avenue; 2nd Floor, Room C-200
Final Exam: Thursday, October 29th (5:00 pm – 6:30 pm)
Course Director: Jason Banfelder (jrb2004@med.cornell.edu)
Teaching Assistants: (qbio1.2015.ta@gmail.com)
Michael LeVine, Anfei Li, Asaf Poran, Mojdeh Shakiba, Yan Zhang
This course will be fully graded: (Honors, High Pass, Low Pass, Fail)

Class Sessions and Lecture Notes

  1. Quantifying a Sample Distribution
    Tuesday, September 1st, 2015

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

  2. Probability Density Functions and the Normal Distribution
    Thursday, September 3rd, 2015

    binomial, Poisson, and normal distributions, testing for normality (part I): an intro- duction to formal statistical tests, testing for normality (part II): qqplots vs. formal tests

  3. Practical R (part I)
    Tuesday, September 8th, 2015

    introduction to R, common data structures (vectors, factors, lists, dataframes), importing data

  4. Confidence Intervals and Contingency Tables
    Thursday, September 10th, 2015

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

  5. p-Values and Formal Statistical Testing
    Tuesday, September 15th, 2015

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

  6. Practical R (part II)
    Thursday, September 17th, 2015

    libraries and ggplot, producing publication quality plots, data driven graphics

  7. Statistical Power and Experimental Design
    Tuesday, September 22nd, 2015

    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. Practical R (part III)
    Thursday, September 24th, 2015

    control structures and programming, the role of simulation in statistics

  9. Multiple Hypothesis Testing and Non-Parametric Tests
    Tuesday, September 29th, 2015

    from Bonferroni to False Discovery Rate, dealing with non-normal data

  10. Bayesian Methods
    Thursday, October 1st, 2015

  11. Correlation vs. Linear Regression
    Tuesday, October 6th, 2015

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

  12. Fitting Model Parameters to Data
    Thursday, October 8th, 2015

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

  13. Practical R (part IV)
    Tuesday, October 13th, 2015

    data wrangling with melt, dcast, and plyr

  14. Quantitative Comparison of Models
    Thursday, October 15th, 2015

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

  15. Final Exam
    Thursday, October 29th, 2015

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