Python for Bioinformatics: 5-Day Course Overview

Instructor: Dr. Martin Jones, in collaboration with the Hub for Applied
Bioinformatics (KCL).

Audience: Biologists with no prior programming experience who want to
learn Python for bioinformatics.

Course Highlights:

Beginner-Friendly: No programming experience required; tailored for
complete beginners with a biology background.

Practical Focus: Real-world bioinformatics examples and hands-on
exercises.

Comprehensive Resources: Electronic copies of presentations, exercises,
data, and scripts provided.

Goal-Oriented: Equip students to apply Python to their research and
continue learning independently.

Who Should Attend?

Designed for researchers and technical workers in biology who:

Have a basic understanding of biological concepts (e.g., DNA, protein
sequences, translation, introns/exons).

Want to learn programming from scratch.

Requirements: A laptop with Python installed; no advanced computer
skills needed.

Course Structure

Session 1: Introduction and Basics

Overview of Python and its benefits for research.
Fundamentals: terminals, variables, strings, and error handling.
Practical: Simple scripts for sequence manipulation.

Session 2: File Handling and Slicing

Reading/writing files and Python's interaction with the OS.
Practical: File processing scripts using slice syntax.

Session 3: Lists and Loops

Handling large datasets with lists and loops.
Practical: Working with larger data files.

Session 4: Conditions and Flow Control

Decision-making with conditional tests and Boolean logic.
Practical: Filtering challenges with CSV files.

Session 5: Structuring Code with Functions

Writing reusable functions and introducing automated testing.
Practical: Creating functions for unit tests.

Session 6: Standard Library and Regular Expressions

Exploring Python's standard library and regex for pattern matching.
Practical: Solving bioinformatics problems with regex.

Session 7: Dictionaries

Introduction to key-value data with dictionaries.
Practical: K-mer counting and DNA-to-protein translation.

Session 8: File Management

Automating file operations like renaming, moving, and organizing.
Practical: Managing DNA sequences by length.

Sessions 9-10: Workshop Time

Recap of key topics or applying Python to personal research.

Contact Information

For questions, email Dr. Martin Jones: martin@pythonforbiologists.com.

For more information:
https://pythonforbiologists.com/introduction-to-python-for-biologists.html

To sign up:
https://estore.kcl.ac.uk/conferences-and-events/academic-faculties/faculty-of-life-sciences-medicine/applied-bioinformatics/python-for-biologists-with-martin-jones-in-partnership-with-the-hab

Jazmine Portch
Operations Assistant for Mathias Gautel
Administrator for Hub for Applied Bioinformatics
School of Basic and Medical Biosciences | Faculty of Life Sciences
and Medicine

Jazmine Portch <jazmine.portch@kcl.ac.uk>

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