By Aleksandra Pawlik, Training Leader.

Last month The Genome Analysis Centre (TGAC) hosted their first Software Carpentry bootcamp. The bootcamp was open to biologists and, in total, 25 of them attended the event. We covered the core Software Carpentry topics, such as using command line to automate tasks, good programming practice with Python, debugging and testing, and version control. We also added an introduction to data analysis with pandas, the Python Data Analysis Library.

The audience turned out to be quite mixed. There were several participants who had never programmed or used command live before, whereas there were others who regularly write code to conduct their research. It is always a challenge to accommodate the needs of such a polarised audience. However, the post-bootcamp feedback questionnaire showed that both beginners and experienced coders found these two days useful. One beginner said that she doesn't program herself at all and doesn't expect it would change much in the future but her main goal was to understand what programming is, as she works a lot with developers. The more advanced attendees were interested to learn about the pandas library and unit testing.

The bootcamp started with TGAC’s Rob Davey teaching command line, with the attendees working on computers at the TGAC Training Lab with the Software Carpentry virtual machine installed. The VM prevented the common problems with setting up the attendees' machines and also provided an opportunity for some participants to use Linux for the first time. The shell module was followed by a lesson on version control. At the end of this module the participants were asked to work in pairs on a repository they hosted on GitHub. Rob Davey's observation on Twitter was "Pushing to someone else's github repository == a lot of excited talk, and some worryingly evil grins". 

At the end of Day 1, we introduced the attendees to programming with Python. We used IPython Notebook for teaching, which most attendees really enjoyed as a tool. It allowed them to interact with the code and see the lecture notes at the same time. However, things got a bit more confusing, especially for the beginners, when we ran the nosetests from the command line.

The bootcamp was very intense and we only managed to make a short introduction to the pandas library. Nonetheless, all bootcamp material was, as usually, made freely available to all attendees in an online and printed version, with the TGAC Events Team doing a great job in preparing all materials in printed binders). The bootcamp finished with an hour-long exercise in which the attendees needed to use the skills they had been taught to fork and clone a repository, fix the broken code in Python and process some files using shell commands. 

In summary, TGAC is keen to intensively develop their training programme and facilities, and so we are looking forward to running more Software Carpentry bootcamps in Norwich.