Software Carpentry for Biomedical Imaging

By Damien Irving.

Earlier this year we got talking to Matthew Dimmock, who is a Lecturer in the School of Biomedical Sciences at Monash University. Biomedical research involves a lot of computer programming these days, however most biomed Masters and PhD students learn very little (if any) programming in their undergraduate studies.

While Research Bazaar HQ is located in the ITS Research Services department at The University of Melbourne, we’d love to see the entire Australian research community benefit from (and contribute to) our efforts to get 21st century researchers using 21st century research tools. When Matthew came to us with the idea of hosting a Software Carpentry biomed bootcamp at Monash Uni, we were therefore more than happy to help out.

For the first three half-days of the bootcamp, we delivered the core Software Carpentry syllabus (i.e. an introduction to the unix shell, programming with Python and version control). The fourth and final half-day was then reserved for a lesson looking at how these basic skills are used by biomedical researchers in their daily work. We like to call these discipline specific lessons “capstone examples,” and Software Carpentry is keen to collect and maintain a large library of examples for many different research disciplines.

If you’d like to run a Software Carpentry bootcamp for your specific discipline, please get in touch. Partnerships like the one we struck with Matthew are exactly what we’re looking for - we can help you by teaching the core Software Carpentry syllabus, and you (as an expert in your discipline) can help us (and the researchers in your field) by developing and delivering a capstone example that can be added to the Software Carpentry repository of teaching materials. 



Research can be ‘bazaar’, we’re here to help! Don’t understand how? Read our mission statement. Flick us a tweet, watch a video, check out our page and follow our blog posts - both formal and fun. Even better than the virtual, meet like minded researchers at one of our events. Come engage with the Melbourne research community!

Get started by contacting your discipline’s 'Research Community Coordinator’, who can help you learn new tools and have fun collaborating with fellow researchers. Here’s the full list.