Python for Biologists

Programming for Scientific Computing


Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.

Next session: Jan 2018

Instructors

  • Tjelvar Olsson
  • Matthew Hartley

Audience

For beginners interested in using Python to solve problems in Biology.

Overview

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 create a script that can read a FASTA file and calculate the GC-content of each sequence in that file.

Schedule

Day 1
9:30 Start
11:00 Coffee break
13:00 End
Day 2
9:30 Start
11:00 Coffee break
13:00 End

Learning outcomes

By the end of the course you should be able to:

Pre-requisites

No previous experience is needed although some basic familiarity with programming and/or the Linux command line would be beneficial. As the course is structured around the participants working through course material a certain degree of curiosity and self motivation is required along with a willingness to ask for help and clarification when required.

Full course syllabus

Course materials

Course book