wiki:scripting

Linux and basic scripting

This course is designed for researchers, including PhD students and postdocs, who frequently handle large datasets or large numbers of files (images, sequence reads, mass spectra etc.) and who needs a more efficient way of working with such data. The course is equally suitable for those working with Windows, Mac OS X or Linux. No prior knowledge of operating systems is needed, the course includes an optional introduction to Linux and an installation practical for Windows and Mac OS X users.

The goal of the course is to empower students and researchers with backgrounds in biology or biomedicine to navigate, manage and perform operations on files and data and metadata in tabular text formats. The data may be microscopy images, FASTA sequences, gene ontology files, chromatograms, mass spectra or tables with data on genes or proteins. The course is not a general introduction to programming and will not deal with XML data, Web services or more advanced topics.

Material

The program.
Command line cheat sheet.
AWK cheat sheet.
Learn, build, & test Regular Expressions.

Monday, January 26

Operating system basics - Jeroen Laros.
File systems, users, ownership and permissions - Maarten van Iterson.
Practical 1: handouts.
The Bash shell and common command line tools - Rob Marissen.
Connecting to other machines - Martijn Vermaat.
Practical 2: handouts.
Installing and updating software - Zuotian Tatum.

Tuesday, January 27

Regular expressions - Tugce Güler.
Introduction to AWK - Magnus Palmblad.
Practical 3: data.
sed, grep rename - Martijn Vermaat.
Shell scripting - Zuotian Tatum.
Practical 4: handouts, example solutions.
Evaluation, wrap up - Jeroen Laros.

Further reading

Online book on AWK.
Online book on Bash shell scripting.

Last modified 2 years ago Last modified on Jan 27, 2015 3:48:52 PM

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