Winter 2025

Lecture: Tuesday/Thursday 10:00-11:20am, ALS 4000

Help Session: Wednesday (1-3pm), Cordley 2212

Course Description

Introduces the fundamentals of data science with specific application to biology. Through a practical, problem-based approach, students will examine the theory and practice underlying widely used computational methods in biology. They will develop mastery in the analysis and visualization of large data sets using Python, with applications to genomics, ecology, and other areas of biology. Students will test hypotheses, infer dataset parameters, and make predictions via broadly applicable data science tools.

Syllabus & Course Policies

Instructor

Timothy Warren
tim.warren AT oregonstate.edu

Course Assistants

Instructor 1
Nate Davidson (Head TA)
davidson AT oregonstate.edu
Instructor 4
Alex Maharjan
maharjaa AT oregonstate.edu
Instructor 4
Andrea Schiffer
schiffan AT oregonstate.edu
Divi
Sarah Hoekema
hoekemas AT oregonstate.edu
Vini Karumuru
Vini Karumuru
karumuruv AT oregonstate.edu

Quiz 1 Review questions:

Class notes

BDS 310 class notes

Weekly Calendar

Date Topic Relevant Reading Assignment
Week 1
01/07, 01/09       
Course Goals and Philosophy
Unix Shell Scripts
Introduction to Pandas     
Jupyter Notebook           
Unix Shell
Python Examples    
Pandas 10 min Reference
Pandas tutorial
HW0 (for students who did not take BDS 310) Due Fri 1/10
HW 01
Due Fri 01/17    
       
Week 2
01/14, 01/16
Analyzing Tabular Data with Pandas
Time Series and Visualization
HW 2
Due Fri 01/24
       
Week 3
01/21, 01/23
Pandas synthesis;Introduction to Random processes matplotlib tutorial
Edward Tufte
Data Visualization textbook
HW 3
Due Fri 01/31
       
Week 4
01/28, 01/30
Application of Random processes: Permutation Testing Inferential Thinking: Chapter 11: Testing Hypotheses
Chapter 12: Comparing Two Samples
Illustrated permutation test
HW 4
Due Fri 02/07
       
Week 5
02/04, 02/06
Resampling for hypothesis and estimation - the bootstrap Chapter 12: Comparing Two Samples
Illustrated permutation test
Chapter 13: Testing Hypotheses
Bootstrap schematic
News article on origin of bootstrap
HW 5
Due Tue 02/24
       
Week 6
02/11, 02/13
The boot strap continued Quiz 1 02/13 [Postponed until 2/18]

 
       
Week 7
02/18, 02/20
Introduction to building and testing models for prediction

Regression and Correlation
Quiz 1 02/18]  
       
Week 8
02/25, 02/27
Regression; Error-minimization for Model Fitting   HW 06
Due Tue 03/04
       
Week 9
03/04, 03/06
Introduction to Optimization and Machine Learning QUIZ 2 3/06  
       
Week 10
03/11, 03/13
Putting it all together   HW 07
Due Tues 03/18