22118/22168 Advanced Unix & Python for Bioinformaticians

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Prepare for the course

You must read and follow the Course preparation before the you show up on the first day of the course.
You are required to read at least the first part of Aligning expectations when the course starts and whenever you have a question related to the conduction of the course.
Resources can be good to check out during the course, or when you need something more.

Teacher: Peter Wad Sackett, pwsa@dtu.dk
Language: The course is taught in English.
Tools: There is Course preparation.
Textbooks: There are no text books for the course. I will make do with powerpoints and references to online resources. You can find the material under the individual lessons in the programme.
Location: Building 116, aud. 83
Time: Monday 13:00 - 17:00, module F2-A.
Deadlines for project work and exam: See the Programme.

Course details

Programme Spring 2025
Aligning expectations Required reading
Code construction Required reading for peer evaluation
Project list Of projects to do
Mini projects For practicing programming

Resources

Unix/Linux

Python 3

  • Online: Coursera course: Programming for Everybody is a beginner course in Python. Everyone who wants to prepare more for course 22118 can start here. The Coursera textbook
  • Online: PYnative Good site for learning about Python. Information, tutorials, exercises and even online editor, all well explained in an accessible way.
  • Youtube: Python beginner course
  • Online: Clean Code by Lukasz Dynowski. An amazing read that is mandatory. Read it once around lesson 3 and once more around lesson 6.
  • Online: Rosalind project Python exercises at different levels for practicing
  • Book: Learning Python, 5th ed. by Mark Lutz (O'Reilly) ISBN: 978-1-449-35573-9. This is the best Python book I have read. It covers all the basics and then some. All from the perspective of being a novice programmer. However, it is a brick; big, heavy and unwieldy. If you only want one Python book, then this should be the one. The course will not be taught from this book, but it could be good to have as a Python reference manual.
  • Book: Python Crash Course: A Hands-On, Project-Based Introduction to Programming by Eric Matthes (No Starch Press) ISBN: 1593276036, 9781593276034. A pretty OK book which leads you into the Python world without too many distracting points and theoretical contemplation.
  • Online: Official Python 3 tutorial
  • Online: Python 3 reference manual
  • Online: Python 3 standard library

Biological

Writing reports, articles, thesis at university level

Interesting but less teaching oriented material

Archive of old course programmes

None yet

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