Teaching basic lab skills
for research computing

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Hi Greg and Adina!

Two days ago I filled out the Software Carpentry survey which asked me, among other things, how much time I had saved using my new Software Carpentry skills. I filled out the I had not really saved that many hours yet (but that I was approaching computational problems in a different way and began implementing version control!).

However, that number of hours changed dramatically later that evening! In preparation for a talk I will give at a conference in a few weeks I was re-doing some analyses. I came to one which was very painful to me because it required using 3 different python scripts for several different files and repeating this for a range of numbers (so we're talking running 3 scripts about 20 times). I did not find this particular analysis very useful or informative, but it really makes my supervisor happy so I thought I should at least try to be a silver (or bronze) student and give it a whirl.

I started to do this analysis the way I had previously done it, by using the script at the command line, figuring out where the files were that I wanted and then waiting for each manipulation to finish before starting the next one. BUT then I realized that you folks had taught me a different way! I made a bash script to use these 3 scripts together and then I even made it successfully loop through all the range of values! I saved so much time (hours at least on this one analysis and lots of mental anguish), have a clear record of what was done and feel so excited to automate more of the complex analysis I'm doing. I feel like I am looking at these problems differently and it is starting to seem a bit clearer! So a huge THANK YOU! I am also going to discuss at my next lab meeting some of the concepts we discussed in the workshop!


Julia (PhD candidate, University of British Columbia)

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