BDS 311 - Computational Approaches to Biological Data

Winter 2026

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

Recitation Section 1: Wednesday 1-2pm (2-2:30 pm help session), Cordley 2602

Recitation Section 2: Wednesday, 2-3pm (3-3:30pm help session, Cordley 2424

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

### Course Assistants

Andrea Schiffer (Head CA)
schiffan AT oregonstate.edu

Steven Cai
caist AT oregonstate.edu

Sarah Hoekema
hoekemas AT oregonstate.edu

Morgan Miller
morgan.miller AT oregonstate.edu

Imre Rist
risti AT oregonstate.edu

Class notes

BDS 310 class notes

Weekly Calendar

Date	Topic	Relevant Reading	Assignment
Week 1 01/06, 01/08	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 1/09 HW 01 Due Fri 01/16

Week 2 01/13, 01/15	Analyzing Tabular Data with Pandas Time Series and Visualization		HW 2 Due Fri 01/23

Week 3 01/20, 01/22	Pandas synthesis;Introduction to Random processes	matplotlib tutorial Edward Tufte Data Visualization textbook	HW 3 Due Fri 01/30

Week 4 01/27, 01/29	Application of Random processes: Permutation Testing	Inferential Thinking: Chapter 11: Testing Hypotheses Chapter 12: Comparing Two Samples Illustrated permutation test	HW 4 Due Fri 02/06

Week 5 02/03, 02/05	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 Fri 2/20

Week 6 02/10, 02/12	The boot strap continued	Quiz 1 02/12

Week 7 02/17, 02/19	Introduction to building and testing models for prediction Regression and Correlation

Week 8 02/24, 02/26	Regression; Error-minimization for Model Fitting		HW 06 Due Tue 03/04

Week 9 03/03, 03/05	Introduction to Optimization and Machine Learning	QUIZ 2 3/05

Week 10 03/10, 03/12	Putting it all together		HW 07 Due Wed 03/18