Programming in Python for Bioinformatics, 7.5 credits

Contents

A practical introduction to Python targeting bioinformaticians, focusing on processing biological data, writing scripts and command-line tools, using relevant packages, and managing workflows. Includes work with text files, data structures, packages, tooling, and interactive computing environments.

Expected learning outcomes

Knowledge and understanding

• Explain fundamental programming concepts (e.g., data types, loops, conditionals, functions, objects, references).
• Explain the basic syntax and semantics of Python.

Skills and abilities

• Process biological data in common file formats (e.g., FASTA, GFF).
• Write structured Python code for bioinformatics problems.
• Use workflow management systems to automate analyses.
• Work in interactive computing environments.

Judgement and approach

• Critically evaluate Python-based bioinformatics analyses.

Required Knowledge

At least 60 completed higher education credits in biology, biomedicine, molecular biology, molecular ecology, molecular evolution, genetics or related fields are required. These must include at least 7.5 credits in bioinformatics; 15 credits in molecular biology, molecular ecology, ormolecular evolution; 7.5 credits in biochemistry, chemistry, mathematics, or statistics; and 7.5 credits in genetics. English 6/level 2.

Form of instruction

Teaching consists of lectures, instructor-led exercises, and computer practicals.

Teaching is normally in English but may be conducted in Swedish if there is no need for English. Each student must have access to a personal computer with internet connectivity and the ability to install required software.

Examination modes

The course is assessed through written assignments and an individual oral examination. The overall course grade is U (Fail), G (Pass), or VG (Pass with Distinction). To pass the course (G), all assessments must be passed. To receive VG, all assessments must be passed and the oral examination must be graded VG.

Adapted examination
For a student who has a decision regarding recommended support due to a disability, the examiner may decide to deviate from the course syllabus examination format. Individual adaptation of the examination format should be considered based on the student's needs and the expected learning outcomes of the course. For more information, see the Procedures for Support for Students with Disabilities and the Rules for Grading and Examination.

Transitional provisions

If the syllabus ceases to apply or undergoes major changes, students are guaranteed at least three examination opportunities (including the regular opportunity) according to the syllabus under which they were originally registered, for up to two years after the previous syllabus ceased to apply.