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Software Carpentry at GARNet

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Software Carpentry at GARNet

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Aleksandra Pawlik

Aleksandra Pawlik

SSI fellow

Posted on 2 May 2014

Estimated read time: 4 min
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Software Carpentry at GARNet

Posted by a.pawlik on 2 May 2014 - 9:40am

By Aleksandra Pawlik, Training leader.

The University of Warwick hosted its first Software Carpentry bootcamp this month. The bootcamp was organised by GARNet which is a UK-based research network for the UK Arabidopsis community (a plant which is for botanists what the fruit fly is for biologists). GARNet facilitates collaboration and interaction between different researchers and supports skills development.

The bootcamp was open to all researchers from the domain and many of the 32 participants came from outside of Warwick. By far the furthest to travel was Christina Koch, who is based in Vancouver and helped co-instruct. The other instructor was Aleksandra Pawlik from the Software Sustainability Institute.

The two main organisers, Charis Cook and Lisa Martin did an amazing job making sure everything was in place for the bootcamp. The attendees received a booklet with all essential information about the event. Everyone had a chance to discuss and network during the dinner at the end of day one (which was topped up with some fancy dessert).

The three helpers Leonor Garcia-Gutierrez, Krzysztof Polanski and Jason Piper made sure that things ran smoothly. The participants were working either on Windows machines or Macs (with a slight prevalence of the latter). Some machines were problematic when it came to the setup, but thanks to the helpers everyone got all the necessary software up and running.

The pre-bootcamp questionnaire showed that around a half of the participants had no, or very little experience, with programming. Several had not used the command line. For that reason, the module on using command line started by explaining the basics of the environment and simple commands. At the end of this session, Christina taught everyone how to write and run shell scripts. The power of the shell turned out to make a very convincing argument for the use of the command line. The only problem we encountered was the fact that the chmod command is not supported on GitBash which many of the attendees were using.

The version control module started at the right pace for everyone to follow. This was a new topic for almost all the attendees. However, when we moved to working with remote repositories on GitHub, we realised that we needed more time. Git is not an easy way to start with version control and maybe this particular module should be extended with bootcamps - like ours - where most of the audience is new to the topic.

The introduction to programming with Python was taught using the IPython Notebook, which everyone liked (although some attendees were convinced we were working online, because the Notebook open in a browser). Day two of the bootcamp covered more programming with Python and an introduction to the Pandas library. Using the latter, we showed the participants how to easily manipulate large csv files, which is a valuable lesson because they are likely to use these in their everyday research.

The bootcamp finished with Christina discussing debugging and testing. Then the participants were given a final exercise in which they had to fork a repository with an unfinished piece of Python code (which also included a small bug). The point of the exercise was to give the attendees an opportunity to see how the skills they learnt separately over the course of two days could be combined in one task.

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