BINF 2111: Course plan
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|