Course

Bioinformatics with Linux and Python

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.

Organised by Wageningen Institute for Environment and Climate Research (WIMEK), Food Technology Agrobiotechnology Nutrition and Health Sciences (VLAG)
Date

Thu 3 December 2020 09:00 until Fri 18 December 2020 12:30

Duration Mornings (9:00-12:30) on 3, 4, 7, 8, 9, 10, 14, 15, 17 and 18 December
Venue Online (Microsoft Teams)

Course level
Entree 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 size
12-15 participants

Intended credits
1.5 ECTS

Course fee
• WUR PhDs with TSP and WUR postdocs registered with WUR graduate schools: €280 (early bird) / €330 (regular)
• SENSE PhDs with TSP: €560 (early bird) / €610 (regular)
• All other PhD candidates: €640 (early bird) / €690 (regular)
• Staff of WUR Graduate Schools/ graduate schools mentioned above: €640 (early bird) / €690 (regular)
• All others: €680 (early bird) / €730 (regular)

Lecturer(s)
Dr. Martin Jones (founder of Python for Biologists)

More information
Peter Vermeulen
e-mail: peter1.vermeulen@wur.nl
tel: +31 (0) 317 48 5090

Registration form
Registration is open for applicants of the former, cancelled edition only. Others can register from the 28th of October onwards.

Registration deadline  
Early bird deadline: 15 November 2020
Final deadline: 26 November 2020

Course organization
WIMEK 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