PM-21 Python für die Biowissenschaften / Python for the Biosciences¶

Instructors: Andrew Straw
Tutor: Michael Harrap

Course content¶

Basics of Python programming
Introduction to version control and command line
Introduction to key data science concepts
Introduction to biological sequence analysis

Who am I (what do I know about programming, data science, and bioinformatics)?¶

strawlab.org

Course format¶

This course will be done in person but can be followed remotely. Lectures will be recorded and uploaded to Ilias shortly after class. Discussion and live particiaption will be encouraged. Friday lectures will start at 10:15. The exercises are self-paced and the tutor will available during our exercise time - Monday afternoons starting at 14:15 to 18:00 - to discuss.

Feedback¶

We would like to make this course as productive as possible for you. Therefore, we encourage any feedback. This can come after the course is over as part of the official Uni Freiburg course feedback. Additionally, we would be happy to get suggestions and ideas as the course is ongoing.

Communication with instructors and tutors during the course¶

We have started a forum room on Ilias. For questions, use this, or ask during the lecture. This lets other students see them and learn from the answers. Almost certainly you will not be the only one with a particular question!

If you email us, unless the content is very personal, we may re-post the question into the forum room so everyone has a chance to benefit from the communication.

Team work¶

We highly encourage teamwork during this course! You are welcome to discuss any aspect of the course with your colleagues. If you have any ideas how to better support teamwork, please let us know.

Grading¶

To pass the course, you must actively participate. This will be checked by verifying that you did the exercise assignments. We have a threshold of 80% of assignments submitted to receive a pass grade.

Assignments¶

Around the time of each lecture, there will be a new assignment posted on Ilias. We expect that you should be able to finish the exercise by Monday at 18:00, but the exercises will be due Wednesday at 23:55. We use https://strawlab-rp2.zoologie.uni-freiburg.de to handle distributing and collecting work. This runs software called forgejo which approximates other sites such as GitHub and is widely used in the software world.

Anaconda and Python installation¶

We would like to you to run Python on your own device if possible. Therefore, we recommend that you install Anaconda on your own computer. A demonstration video is available here and we can offer further help during the tutorials.

Ten simple rules for biologists learning to program ¶

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