22113/22163 - Unix & Python Programming for Bioinformaticians
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. 82 NOTICE THIS LOCATION CHANGE
Time: Monday 13:00 - 17:00, Thursday 9:00 - 12:00, module F2-A and F2-B.
Deadlines for project work and exam: See the Programme.
Course details
There are no plans for streaming the lectures as there already are recorded video lectures for first half of the course. Discord is used for online help and discussion - if necessary.
| Programme | Spring 2024 |
| 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
- Youtube: Linux File System/Structure Explained
- Youtube: The Complete Linux Course: Beginner to Power User
- Youtube: Linux series by the very entertaining NetworkChuck
- Online: Online tutorial on unix
Python 3
- Online: Coursera course: Programming for Everybody is a beginner course in Python. Everyone who wants to prepare more for course 22113 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
- PDF: Vejledning i opbygning og skrivning af rapporter
- PDF: Guide on how to write a report
- Online: How to structure a science paper
- PDF: Master Thesis Advice
- Online: How to write a thesis
Interesting but less teaching oriented material
- Blog: Why rewriting software projects can be bad
- Online: Top 12 reasons you know you are a Big Data biologist
- Online: How programming and your life is similar
- Youtube: What most schools don't teach - how to think