a software carpentry perspective of bioinformatics training - scott ritchie

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: dff.melb@gmail.com, @dfflandersScott Ritchie: sritchie73@gmail.com, @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