# Bio 5075 Fall 2020 Syllabus

### SCHEDULE:

2020-09-14
Lecture 0 (Computation): Introduction to Jupyter and Python

• Course format
• Introduction to Jupyter Notebook

2020-09-21
Lecture 1 (Computation): Python Loops and Variables

• Variables
• Lists
• Flow control: FOR loops

2020-09-28
Lecture 2 (Computation): Dictionaries and Conditionals

• Dictionaries
• Flow control: conditional statements
• Coding strategies

2020-10-05
Lecture 3 (Computation): More lists, Reading Files, Functions

• Functions
• File input/output
• List comprehensions and manipulations

2020-10-12

Lecture 4 (Statistics): Summarizing Numbers

• Single number summaries: mean, median, mode
• Two numbers: variance and standard deviation
• Dot plots and histograms
• Distributions

2020-10-19 Lecture 5 (Statistics): Basic Probability

• Intuitive probability estimation from histograms
• Basic theory and notation
• How probabilities combine: “and” and “or”
• Independence and conditional probability
• Counting successes and failures

2020-10-26

Lecture 6 (Statistics): Simulation and Hypothesis Testing (I)

• Why simulate?
• Hypothesis testing and the null distribution
• What p-values are and are not
• Recent controversies in the use of p-values

2020-11-02
Lecture 7 (Computation): Compound data structures, Plots

• Lists of lists, dictionaries of lists, etc.
• Matplotlib

2020-11-09

Lecture 8 (Computation): Numpy arrays

• Numpy arrays vs lists

2020-11-16

Lecture 9 (Computation): Pandas, Bioinformatics

• Pandas dataframes
• IO

2020-11-23

Lecture 10 (Statistics): Simulation and Hypothesis Testing (II)

• Permutation testing
• Sampling from a population
• Bootstrap confidence intervals
• Bootstrap hypothesis testing

2020-11-30
Lecture 11 (Statistics): Power Analysis, Experimental Design, and Parametric Statistics I

• Statistical Power
• Paired tests
• The standard error and the t-test
• ANOVA

2020-12-07
Lecture 12 (Statistics): Power Analysis, Experimental Design, and Parametric Statistics II

• Chi squared tests

FINAL HOMEWORK DUE Tuesday, December 15.