Skip to main content

Programme

The taught components will be drawn from Software Carpentry via "live coding", with the instructor typing commands and the attendees following along. There will be various practicals interspersed throughout.

Delegates must be familiar with the Unix shell before the workshop. There are easy to follow tutorials on the Software Carpentry website: http://software-carpentry.org/v4/shell/index.html

We’re pleased to confirm our instructors, Aleksandra Pawlik (Software Sustainability Institute) and Christina Koch (University of British Columbia). Local helpers will be: Leonor Garcia-Gutierrez, Krzysztof Polanski and Jason Piper, all PhD students from the University of Warwick.

The programme and tutorials for the workshop can be found here: http://apawlik.github.io/2014-04-09-GARNET/

Day 1

09:45-10:00 Introduction to GARNET, iPlant, Software Carpentry, the tension between research and software development, and what will be covered during the workshop.

10:00-10:30 Installation: Ensuring attendees’ laptops are set up with the tools they need.

10:30-12:30 Version control 1

13:30-15:30 Version control 2

15:45-17:45 Introduction to programming using Python: Introducing basic Python types, lists, conditionals, loops, functions, command-line arguments, importing modules and Python scripts. Also covers good programming practice in terms of naming variables, commenting and functions. Assumes no programming experience.

17:45 Hot buffet dinner and wine reception

Day 2

09:00-11:00 Further Python: recap and more tutorials

11:15-13:15 Data management and scientific programming using Python

14:15-15:15 Designing and testing code: Introduction to the principles and practice of designing testable code, defensive programming, and writing and running tests.

15:15-16:00 Consultancy and/or final exercises

SPONSORS

We are grateful to the Company of Biologists and the Software Sustainability Institute/Elixir UK for support of the workshop.

3_cob1c_logo_73.jpg ssi.png