Scripting for Life Science Researchers

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 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.

Knowledge of Linux is required to attend this course!


Program and material

Day 1

Time Location Activity Teacher
11:00 V4-36 Introduction Mihai
11:30 V4-36 Basic scripting Mihai
12:00 V4-36 Practical 1
13:00 Lunch
14:00 V4-36 Advanced scripting I Jeroen
14:30 V4-36 Practical 2
15:00 Pause
15:15 V4-36 Advanced scripting II Jeroen
15:45 V4-36 Practical 3
16:15 Closing

Day 2

Time Location Activity Teacher
11:00 J1-83 Processes and Job Control Jonathan
11:30 J1-83 Practical 4
11:45 Pause
12:00 J1-83 Regular Expressions Yassene
12:30 J1-83 Practical 5
13:00 Lunch
14:00 J2-25 Text Processing Jonathan
14:30 J2-25 Practical 6
15:00 Pause
15:15 J2-25 Introduction to AWK Magnus
15:45 J2-25 Practical 7
16:15 Closing

Past sessions

12-13 September, 2017

  • Time: 11:00 - 16:30
  • Location: 03-V-04-036, 01-J-01-083, 01-J-02-025
  • Teachers:
    • Jeroen Laros
    • Magnus Palmblad
    • Jonathan Vis
    • Yassene Mohammed
    • Mihai Lefter

About this repository

The presentations are made in LaTeX, there are two submodules on which this repository depends.

The website directory is for storing the compiled presentations, handouts and program. A Trac wiki markup file contains the website content. Uploading, updating and adding attachments can be done easily with the tracwiki program.


After cloning this repository, fetch the data from the submodules by issuing the following two commands:

git submodule init
git submodule update

(More on Git submodules)

A new presentation can be added like this:

cd .submodules/presentation
bash mkpres.sh ../../mypresentation

Pictures in the presentation can be made available by adding a symbolic link to the presentation-pics repository.

ln -s ../.submodules/presentation-pics/pics/somepicture.png

The Makefile will take care of converting this picture to the correct format.