Teaching basic lab skills
for research computing

Carpentry week 2016 at the University of Oslo

Cross-posted from the author’s blog.

In March 14-18 2016 we organised the first Carpentry week at the University of Oslo. After a mini-Seminar on Open Data Skills, there was a Software Carpentry workshop, two Data Carpentry workshops and a workshop on Reproducible Science as well as a ‘beta’ Library Carpentry workshop.

The Software and Data Carpentry effort at the University of Oslo, aka ‘Carpentry@UiO’, really started in 2012 when I invited Software Carpentry to give a workshop at the university. The then director, Greg Wilson, came himself and gave an inspirational workshop – recruiting Karin Lagesen and I to become workshop instructors in the process. Karin and I graduated from instructor training spring 2013 and have been giving a couple of workshops in Oslo and elsewhere.

In the fall of 2014 we partnered with the UiO Science Library (Realfagsbiblioteket) with the goal of giving regular workshops and to recruit more people as helpers and instructors. Before Carpentry Week, we have held 4 workshops, and 10 helpers and instructors became involved.

In connection with the 4th birthday of the Science Library, we together came up with the plan to organize a mini-workshop on Open Data Skills (the video recording is here), followed by four days with five workshops with a total of 90 participants. We were very fortunate to have three international instructors coming all the way to Oslo for these events: Tracy Teal, executive director Data Carpentry; Leah Wasser, supervising scientist at The National Ecological Observatory Network (NEON); and Titus Brown, assistant professor at UC Davis. Tracy, Leah and Titus, thanks for coming!

The workshops we offered were:

  • A Software Carpentry workshop teaching automating tasks with the Unix shell, collaborative code development through version control with git and github, and modular code design with python, with 10 participants; this workshop was taught by Halfdan Rydbeck, Hugues Fontenelle, Arvind Sundaram and Axel Rosén
  • A Data Carpentry workshop for GeoSciences and others, focussing on spatio-temporal data, the use of shell for data exploration and data analysis and visualization using R, with 10 participants, taught by Leah Wasser, Michael Heeremans and Anne Fouilloux
  • A Data Carpentry workshop for Biosciences/Genomics teaching about metadata, use of the shell and cloud computing, and data analysis and visualisation using R, with 29 participants, taught by Tracy Teal, Carrie Andrew and Lex Nederbragt
  • A ‘beta’ version of a Library Carpentry workshop teaching about version control with Git and GitHub, tech jargon, working with plain text formats using Sublime Text, APIs, regular expressions, use of the shell, and data cleaning using OpenRefine with 28 participants, taught by Leon du Toit, Elin Stangeland, Live Kvale, Kyrre T. Låberg, Ahmed Abdi Mohammed, Mari Lundevall, Stian Lågstad and Dan Michael O. Heggø.
  • A one-day workshop teaching technologies such as make, Jupyter Notebooks, Docker, myBinder and RMarkdown/Knitr for making computational analysis more reproducible, with 13 participants, taught by Titus Brown and Tracy Teal

Carpentry Week gave a real push to the effort at UiO, generating a lot of attention and allowing us to recruit several new helpers and people interested in becoming instructors. At the Mini-Seminar, we proudly announced that the University of Oslo joins the Software Carpentry Foundation as an affiliate. Affiliate status enables us to strengthen the effort at UiO, help grow the Foundation, and gives us easier access to instructor training.

For me personally, the Carpentry Week was a fantastic experience. It was very satisfying to see so many undergraduate and graduate students, postdocs and other staff coming to the workshops – we clearly are addressing a need for this kind of skills training. This was the first time I experienced – and instructed at – a Data Carpentry workshop. As I suspected, many researchers I interact with need the kind of training these workshops offer – perhaps even more so than what Software Carpentry offers. I don’t have many possibilities to teach with experienced instructors not from UiO, so witnessing both Tracy Teal and Titus Brown gave me a excellent opportunity to reflect (positively) on my own teaching.

Finally, Software and Data Carpentry attract a fantastically open, warm and welcome community of scientists and students, and we see the same happening at UiO. Instructors and helpers are a great bunch of people to work with!

The Carpentry@UiO initiative wants to thank the Science Library, whose excellent organizational skills made putting together so many workshops a breeze. The Library provided the indispensable organizing efforts that such events require, as well as coffee and tea, fruit during the workshops, and lunch for everyone participating each day. Live Rasmussen and coworkers, you are fantastic! Let’s do this again next year…

Upcoming workshops at UiO: Software Carpentry and Data Carpentry.

(Thanks also to the Carpentry@UiO instructors who gave feedback to earlier drafts of this post.)

UNIVERSITY OF OSLO

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