Welcome to Bioinformatics 2111/2111L. In this course, you’ll learn how to write simple executable UNIX scripts that automate “pipelines” of bioinformatics software, and to write scripts for genomic data analysis using the Python language.

The course is structured so that you learn to work in the UNIX environment writing shell scripts first. Shell scripting will familiarize you with variables, and elements of control flow, and you’ll also learn something about how to assemble genome sequences. Then we’ll move into Python and use it to manipulate and integrate information from personal genomic variation data and other interesting biological data sources.

Note: this page will be regularly updated with additional calendar information and links — it is your reference for all the course materials outside Moodle.

 

WEEK	Lecture 1	Lecture 2	LAB Activity
WEEK 1	8/25 Course overview, UNIX shell and text editors	8/27 UNIX shell profiles and basic scripting	LAB UNIX shell help session
WEEK 2	9/1 Biology review	9/3 Introduction to genome assembly software workflow	LAB Genome assembly at the command line
WEEK 3	9/8 Scripting for automation	9/10 Basics of variables	LAB Simple genome assembly script
WEEK 4	9/15 Shell conditionals	9/17 Shell loops	LAB Automated script for multiple input files
WEEK 5	9/22 Bash input from a file and intro to variant calling	9/24 Variant calling software workflow	LAB Adapt your bash script to use file input
WEEK 6	9/29 Introduction to python syntax	10/1 Introduction to python syntax	LAB Making the most of genomic annotation with bedtools
WEEK 7	10/6 Conditionals in python	10/8 Opening files in python	LAB Writing your first python script
WEEK 8	10/13 Fall break	10/15 Getting started with python lists	LAB no lab today/catch up week