Introduction to Bioinformatics Scripting and Programming
Note: This is a four credit course which runs for 13 weeks.
This course is a high-content introduction to scripting and programming with applications in bioinformatics. It is appropriate for students with little or no previous programming experience. The course covers the fundamentals of working with Linux systems, using bioinformatics tools, and manipulating biological data files. A variety of scripting languages will be used, including bash, Perl, and Python. The course will also touch on topics such as how to interact programmatically with SQL databases and other client-server systems, and how to work with distributed compute systems to perform large calculations.
At the end of the course, students will be able to:
· Work comfortably with GNU/Linux command-line tools.
· Create simple scripts in bash, Perl, and Python.
· Access large repositories, such as Ensembl, the PDB, and GenBank programmatically.
· Use packages such as BioPerl or BioPython to perform basic bioinformatics tasks.
· Manipulate data from public repositories and common biological data structures.
· Develop and/or modify existing scripts to solve bioinformatics problems.
· Script compute-intensive bioinformatics tasks.