Research School for Socio-Economic and
Natural Sciences of the Environment
Research School for Socio-Economic and
Natural Sciences of the Environment
Agenda

Bioinformatics with Linux and Python

Date: 10 May 2021 - 21 May 2021
Location: online

Course Description

Linux and Python, a dynamic, readable programming language, is a popular combination for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Linux and Python education in a self-directed way.

 This course gives priority to VLAG and WIMEK PhD candidates due to the limited space available. Registration is open for VLAG and WIMEK PhD candidates until the 10th of April. For other PhD candidates: if you are interested, send an email to wimek@wur.nl with the title: Bioinformatics with Linux and Python_interest list. If the course is not full yet on the 20th, we will invite those that have send an email to us on first come, first serve basis.

General information

Course levelEntree level programming. No modelling skills are needed. However, this course is heavy on bioinformatics and programming, so the interest to improve your modelling and programming skills is a requirement.
Group size12-15 participants
Intended credits1.5 ECTS
DatesMornings (09:00-12:30) 10-21 May 2021
Course fee• WUR PhDs with TSP and WUR postdocs registered with WUR graduate schools: €260 (early bird) / €310 (regular)
• SENSE PhDs with TSP: €520 (early bird) / €570 (regular)
• All other PhD candidates: €600 (early bird) / €650 (regular)
• Staff of WUR Graduate Schools/ graduate schools mentioned above: €600 (early bird) / €650 (regular)
• All others: €680 (early bird) / €730 (regular)
Lecturer(s)Dr. Martin Jones (founder of Python for Biologists)
More informationPeter Vermeulen
e-mail: peter1.vermeulen@wur.nl
tel: +31 (0) 317 48 5090
Registration formRegistration form
Registration deadline   Early bird deadline: 10 April 2021
Final deadline: 1 May 2021
Course organizationWIMEK and VLAG

Course programme (subject to small changes):

Session 1 – connecting to the server and basic Linux commands
Session 2 – assembling Linux commands into pipelines
Session 3 – introduction to bash scripting and variables
Session 4 – biological pipelines and data formats
Session 5 – introduction to Python, text and files
Session 6 – lists and loops in Python
Session 7 – conditions in Python
Session 8 – writing functions in Python
Session 9 – paired data and dicts in Python
Session 10 – programming workshop: develop you own ideas

Former occurrences of this course

  • 16-20 March 2020