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Lecturer(s)
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Tolar Nikolas, Mgr.
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Nguyen Petr, RNDr. Ph.D.
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Course content
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Lectures and practicals cover the following topics: 1) Introducing the Shell, basic commands 2) Files and directories 3) Pipes and filters 4) Loops 5) Shell scripts 6) Finding things 7) Introduction to Python, Variables, Logical operations 8) Basic data types, casting, flow control 9) Data import and export, Functions 10) Collection data types, exception handling 11) File handling and Modules 12) Real-life python usage in Bioinformatics, Biopython
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Learning activities and teaching methods
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- Class attendance
- 26 hours per semester
- Preparation for classes
- 25 hours per semester
- Preparation for credit
- 24 hours per semester
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Learning outcomes
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The course presents the basic computing tools needed to build automated and reproducible pipelines for biological data analysis, visualization and publication.
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Prerequisites
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unspecified
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Assessment methods and criteria
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unspecified
credit: attendance at practicals, home assignment
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Recommended literature
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Allesina S, Wilmes M (2019) Computing Skills for Biologists ? A Toolbox. Princeton University Press.
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David M. Beazley, Python Cookbook. O'Reilly Media (2013).
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Haddock SHD, Dunn CW (2010) Practical Computing for Biologists. Sinauer Associates https://swcarpentry.github.io/shell-novice/.
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