Python for Biologists: Programming for Scientific Computing


Python is a flexible programming language that is becoming increasingly popular for scientific computing. The course is is split into 12 modules and runs over two half days. At the end of each module there a number of exercises to help solidify the learning. By the end of day one you will have created a function for calculating the GC-content of DNA sequences. By the end of day two you will have a script for reading in sequences from FASTA files. The final exercise will be two combine the two to combine the two to create a script that can read a FASTA file and calculate the GC-content of each sequence in that file.

Learning outcomes

  • Ability to run Python scripts and work in interactive Python sessions
  • Ability to understand and edit existing Python scripts
  • Ability to manipulate numbers and text
  • Ability to create reusable functions
  • Basic understanding of Python's built-in data types and structures
  • Basic understanding of control flow and loops
  • Ability to read in and write out files
  • Ability to reuse functionatiy from Python's built-in standard library
  • Experience of creating a complex data analsyis script

Full course syllabus

  • Interacting with Python
  • Editing scripts
  • Manipulating numbers
  • Manipulating strings
  • Creating reusable functions
  • Data types
  • Data structures
  • Control flow and loops
  • Reading and writing files
  • Reusing code
  • Parsing FASTA files
  • Linking it all together
  • Further reading

Licence: Other (Not Open)

Keywords: Python for Biologists, John Innes Centre, JIC

Target audience: For beginners interested in using Python to solve problems in Biology.

Authors: Tjelvar Olsson, Matthew Hartley

Scientific topics: Software engineering

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