PPB18 - Programming in Python for Biologists (2018)

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. In particular the sessions will cover:

  • working with DNA and protein sequences
  • data retrieval from files and their manipulation
  • running applications, such as BLAST, locally and from a script
  • finding motifs in sequence
  • parsing common file formats (Uniprot, GenBank, PDB, BLAST) with Biopython
  • ways to find and correct program errors

The course will be highly interactive and the students will continuously put theory into practice while learning.

DOI: 10.5281/zenodo.3813780

Licence: Creative Commons Attribution 4.0 International

Keywords: Bioinformatics, Biology, Biological databases


Additional information

Target audience: Academia/ Research Institution, Industry, Non-Profit Organisation, Healthcare

Resource type: Documentation, Exercise, Handout, Scripts

Authors: The Gulbenkian Training Programme in Bioinformatics

Contributors: Allegra Via, Vincenza Colonna, David Philip Judge

Operations: Data retrieval, Data handling