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: 16 March 2020 - 20 March 2020
Location: Wageningen

FULLY BOOKED

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.


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
Course fee

The fees below include lunch and tea coffee; but not accommodation
• WUR PhDs with TSP and WUR postdocs registered with WUR graduate schools: €350 (early bird) / €400 (regular)
• SENSE PhDs with TSP: €700 (early bird) / €750 (regular)
• All other PhD candidates: €780 (early bird) / €830 (regular)
• Staff of WUR Graduate Schools/ graduate schools mentioned above: €780 (early bird) / €830 (regular)
• All others: €820 (early bird) / €870 (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 is not possible. This course is fully booked.
Registration deadline   Early bird deadline: 16 February 2020
Final deadline: 29 February 2020
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