Practical Python Programming For Biologists

Synopsis

This is a four-day course designed to provide an introduction to the Python programming language for all biologists and life scientists. Throughout the course, participants will learn python programming concepts and practical applications, engaging in hands-on coding exercises and projects to solidify their understanding. 

The course is intended for biologists at all levels (students, researchers, and group leaders) with little or no prior programming experience. The pace of the course will begin foundational and develop into more complex aspects, with lots of time dedicated to the practice of the concepts covered.

Objectives

By the end of the course, participants will be able to:

  • Write and run basic Python code to extract, parse, process, analyse and visualise biological data
  • Understand the basics of bioinformatics libraries in Python
  • Understand the basics of data analysis and statistics using Python
  • Write organised and reusable code
  • Create a simple project using Python for their specific field.

Instructor: Dr. Daniel Pass
Class size: 10-12 people
All days run 9:00-17:00 with 1h break

Schedule

Day 1:

  • Introduction, concepts, & data types
  • Basic data types, first coding, & Data manipulation
  • Collections – Lists & Tuples
  • Project: Manipulating DNA sequences – Transcription Factor Binding

Day 2

  • Collections – Dictionaries
  • Conditionals & loops
  • Advanced string manipulation
  • Project: Field Data wrangling

Day 3

  • I/O handling
  • Organising code into functions
  • Modules and libraries: BioPython
  • Project: Chipseq, bespoke file formats, and functional organisation

Day 4

  • Statistics modules: numpy & pandas
  • Data visualisation packages (matplotlib/seaborn/plotly)
  • Your code as command line programs & argparse
  • Coding in the age of ChatGPT and AI bots
  • Project: More data problem solving – viral genomics
Book an upcoming course