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Scott C Ritchie, Damien Irving, David Flanders Programming is increasingly becoming an essential skill for researchers in the life sciences. However, most scientists doing bioinformatics receive no formal training in programming, inhibiting both research efficiency and reproducibility. Software Carpentry is a volunteer organisation whose goal is to make scientists more productive, and their work more reliable, by teaching them basic programming skills through intensive two-day workshops (bootcamps). In this session we will discuss the Software Carpentry philosophy and reflect on our experiences running bootcamps for bioinformaticians in the Melbourne region. Presented at InCoB 2014 special session on Bioinformatics Education and Training: http://incob2014.org
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Software Carpentry
@ITS_Res: Empowering Communities of Researchers with ITS Services
Scott Ritchie, Ph.D. Student, Medical Systems Biology, Research Community Coordinator,
Software & Data Carpentry Instructor for R
Teaching lab skills for scientific computing
The state of scientific computing“Giving the average scientist access to a supercomputer is like giving the average 16 year old a Ferrari, and the crash rates are similar”
— Greg Wilson, creator of Software Carpentry, PyCon 2014
Software Carpentry• Teach the basic lab skills for scientific computing• Two day bootcamps• Taught by volunteer instructors (and helpers!)
Software Carpentry• Unix/Shell• Python, Matlab, or R• Git + Github• SQL
Software Carpentry: what we really teach• Unix/Shell• Python, Matlab, or R• Git + Github• SQL
Task Automation Modularisation Tracking and Sharing Structured Data
Software Carpentry: what we really teach• Unix/Shell• Python, Matlab, or R• Git + Github• SQL
Task Automation Modularisation Tracking and Sharing Structured Data
FeedbackA two day workshop will save on average, a day a week, for the rest of your scientific career.
Teaching Pedagogy and Instructional Design
1. Wilson, G. Software Carpentry: lessons learned. F1000Res. 3, 62 (2014). 2. Wilson G, Software Carpentry: Lessons Learned. PyCon 2014
https://www.youtube.com/watch?v=FtKO619O5g0
• Scientific computing != software development!• Intrinsic motivation• Instructional Scaffolding• Instructor training: how, not what to teach.
… Carpentry?Skills Required to be a successful Bioinformatician:• Scientific Computing / Programming• Data Analysis / Statistics• Biology
The Research Bazaar• Hosts and funds most of the bootcamps in Australia• Researcher training• How do we apply this paradigm to teach tools in
other disciplines?
Researcher Training Conference
resbaz.tumblr.com/conference
• 3 Days, February 16th–18th • Interactive training sessions• Tools for Open Science and Arts/Digital Humanities
• February 11th–13th
• Learn about the pedagogy of teaching
“Kickstarting doctoral training in Australia”
n e c t a rcloud > virtual labs > research tools
“Train the Trainer” Conference
Find out more
Blog: resbaz.tumblr.comTwitter: @ITS_Res, #ResBazDavid Flanders: [email protected], @dfflandersScott Ritchie: [email protected], @sritchie73
Software Carpentrysoftware-carpentry.org
The Research Bazaar
AcknowledgementsDavid Flanders (Research Bazaar)
Damien Irving (Research Bazaar)
David Lovell (CSIRO)
Extra Slides
Some Statistics1-2
1. Hannay, J. E. et al. How Do Scientists Develop and Use Scientific Software? (IEEE Computer Society, 2009)
2. Prabhu, P. et al. A Survey of the Practice of Computational Science. in State of the Practice Reports 19:1–19:12 (ACM, 2011).
• Scientists spend 40% of their time building or using software
• 55% say this figure is rising
• 96% are largely self taught
