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.

Operations: Data handling, Data retrieval

Keywords: Bioinformatics, Biology, Biological databases

Resource type: Documentation, Exercise, Handout, Scripts

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

Difficulty level: Intermediate

Licence: Creative Commons Attribution 4.0

Authors: The Gulbenkian Training Programme in Bioinformatics

Contributors: Allegra Via, Vincenza Colonna, David Philip Judge

DOI: 10.5281/zenodo.3813780

PPB18 - Programming in Python for Biologists (2018) https://tess.elixir-europe.org/materials/ppb18-programming-in-python-for-biologists-2018 Training Material that covers the basic concepts of Python, such as calculation, organization of data, reading and writing files, program logic and writing larger programs. All the examples and exercises focus on solving biological problems. Allegra Via Vincenza Colonna David Philip Judge Bioinformatics, Biology, Biological databases Academia/ Research Institution Industry Non-Profit Organisation Healthcare