BIF-50806 Practical Computing for Biologists

Course

Credits 6.00

Language of instruction:

English

Continuation courses:

BIF-51306 Biological Data Analysis and Visualization, BIF-51806 Biological Discovery Through Computation

Contents:

This course offers a practical introduction to advanced computer use for the analysis of biological data. It is focused on technical aspects of handling large data files, working on remote computers running the Linux operating system using the command line (shell), and developing practical programming/scripting skills. There will be some emphasis on biological molecules (DNA, proteins, etc.), but the used methods are generally applicable to all biological fields.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- explain fundamental computational concepts
- be proficient in command line (shell) usage;
- analyse biological data using command line tools;
- store biological data in appropriate data structures, like strings, lists and dictionaries;
- apply simple algorithms to filter and simplify biological data;
- write and modify simple computer scripts (in Python) for data analysis and visualization.

Activities:

- computer labs (partly supervised);
- class room exercises;
- self study.

Examination:

50% practical assignments, 50% theoretical exam. The minimal mark for each part of the examination is 5.5.

Literature:

Required: Steven Haddock & Casey Dunn, 'Practical computing for biologists', Sinauer, 2010. ISBN-13: 978-0878933914. The book is required, it is used to prepare for in-class discussions.