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RBIF 100

Bioinformatics Scripting and Programming

This course is a high-content introduction to scripting and programming with applications in bioinformatics. It is appropriate for students with little previous programming experience. The course covers the fundamentals of working with Linux systems, using bioinformatics tools, and manipulating biological data files. The focus will be on scripting with Bash and Python. The course will also touch on topics such as how to interact programmatically with SQL databases and RESTful web services, 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.
Develop and/or modify existing scripts in Bash or Python to solve bioinformatics problems.
Manipulate common biological data structures.
Interact programmatically with public repositories such as Ensembl.
Script compute-intensive bioinformatics tasks.

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