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PBfB introduces students to use general computational tools to work more effectively. It pulls together a broad range of free powerful, and flexible tools that are applicable to geneticists, molecular biologists, ecologists, oceanographers, physiologists, and anyone interested or in need of bioinformatics in their research. It features practical use of bioinformatic techniques to solve real analysis problems..
PBfB will cover the “nuts and bolts” of datacentered computing tasks in a Unix/Linux environment. We will cover the basics of using such an environment, including installing and running software on remote machines. We will make use of command line tools to explore and analyze data, and explore the use of scripting languages such as Python and R to A) write our own analysis tools as needed and B) act as “glue” to make effective pipelines of other tools. We will introduce practical use of databases and how to retrieve data from remote public databases. We will show how to use R for exploring and visualizing data, including GIS tools.
PBfB will use concrete example taken from various field, for example data from Next Generation Sequencing (NGS) technologies in genetics and molecular biology, as well as remote sensing and oceanographic data widely used in environmental ecological and evolutionary biology.
The course will include lectures followed by practical computer exercises and individual assignments. Students will prepare a project assignment in small groups featuring the use of the skills learned during and aiming at solving a concrete example. Students will present and explain their pipeline and results to the group in an oral presentation during the last days of the course.
|Intended credits||5.0 ECTS|
|Course organisation||RSEE - Research School Ecology and Evolution|
|More information||Course website|