Python for downstream data analysis

Python for downstream data analysis

programming
basic bioinformatics
ELIXIR
Location:

Online course

Start date:

21 September 2020

Duration:
21 September 2020
22 September 2020

General context

This course is organised over two full days. We will start with a brief recap of  the basics of Python, followed by exploring several libraries for data manipulation and visualization. With the help of plenty hands-on exercises, you will learn to fetch biological data and sequencing files from online databases, and be able to parse and analyze this data. There will be time to highlight specific requests of topics from participants. 

 

Objectives
  • Use libraries for advanced data manipulation and visualization
  • Working with biological data using Biopython
  • Being able to write scripts and functions from scratch for specific bioinformatics problems
Required skills

Participants are expected to have attended an introductory Python course and/or have acquired some working knowledge of Python.

Trainers

Tuur Muyldermans

Tuur Muyldermans is a bioinformatics trainer at the VIB Bioinformatics Core and ELIXIR Belgium. 

Contact Tuur Muyldermans :
James Collier

James Collier is a professional software developer with >10 years of experience working on software ranging from tiny embedded devices through to high-performance and web applications. He completed his PhD at Monash University on Australia and now works on scientific software within the VIB Bioinformatics Core.

Contact James Collier :

Program

Introduction & Python recap
-
Data manipulation in Pandas
-
Visualization libraries (matplotlib, seaborn, i.a.)
-
BioPython (1/2): introduction & fetching data
-
BioPython (2/2): Parsing and analyzing biological data & file formats
-
Advanced bioinformatics exercises
-

Selected exercises from Rosalind.

Interpreting complex scripts
-

Selected from the BioPython Cookbook

Selected topics from participants
-