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Software Carpentry for NHS Clinical Bioinformatics course

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Software Carpentry for NHS Clinical Bioinformatics course

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Aleksandra Pawlik

Aleksandra Pawlik

SSI fellow

Posted on 11 November 2015

Estimated read time: 3 min
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Software Carpentry for NHS Clinical Bioinformatics course

Posted by a.pawlik on 11 November 2015 - 5:49pm

By Niall Beard, myGrid, University of Manchester

On 9th and 10th November myself and Ian Dunlop (also myGrid, University of Manchester) taught at a Software Carpentry workshop for 12 NHS trust Informaticians. The workshop was a part of the MSc in Clinical Bioinformatics course led by professor Andy Brass at the University of Manchester. The workshop followed up a success of the same training delivered for was  for the last year's student cohort. This year as well, the feedback was very positive.

Ian and I had our first experience teaching and were both impressed by how enthusiastic and engaged the students were. In only two days, we got through a considerable amount of content such as file navigation and manipulation in the command line; mastering the basic Git workflow; parsing XML files; and writing tested and documented Python code. 

We asked questions regularly to keep our students engaged and were amazed to find they not only had the correct answers, but had more questions to ask us; which showed a great comprehension of the topics covered. Using VM images meant setup time was minimal and there was none of the unexpected environmental issues that trainers face when trainees bring their own laptops. We got our students to create new git repositories for every program they made and had them periodically push them to GitHub to reinforce the Git workflow. We thought it best to impress on them not just how to use Git, but when to.
Best bit: Pairing up students to try and make merge conflicts using GitHub. This got everyone's energy up and had them helping one another understand what they were doing. Worst bit: Having a hard time with the Overlapping Ranges example in the Testing chapter. With little time or energy left and a somewhat convoluted example - it was hard for trainers and trainees alike to get their heads around the program.

We were short of time towards the end and found ourselves wearily pushing through the final chapters. Having another day would have been nice - but given the time we had and the progress the students made - I think it was an all round successful Software Carpentry course.​

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