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Tuesday, May 14, 2019

June Workshop: Writing reproducible and executable scientific papers with R and Python

The eScience Institute Special Interest Group on Reproducible Research and Open Source Software and the UW Libraries are pleased to announce a joint workshop on "Writing reproducible and executable scientific papers with R and Python." This workshop is the signature event of the two groups, and its goal is to increase the transparency and reproducibility of research conducted at UW. 

We invite UW researchers at any level (undergraduate, graduate, post-doctorate, staff, faculty, etc), from any part of campus who want to learn more about how to use cutting-edge technologies to make their papers and publications more reproducible. This workshop is aimed at researchers who write empirical journal articles and want to make it easier for others assess the validity of their work, reuse their work in new research, and enhance public trust in research.

The workshop will feature high-level overviews of, and hands-on tutorials with, these four technologies that support reproducible research:
  • Binder with Chris Holdgraf: an open community and open-source in-browser cloud service that lets users create shareable, interactive, reproducible environments running a wide variety of interfaces (such as Jupyter or RStudio) based on the contents of the GitHub repository.
  • Stencila with Nokome Bentley: a stand-alone platform for creating, collaborating on, and sharing data-driven content by writing documents with code cells that link to live output, and is accessible to non-coders
  • Whole Tale with Craig Willis: an in-browser cloud service that provides a Juypter notebook or RStudio server instance based on the contents of a DataONE data repository
  • Code Ocean with Seth Green: an in-browser cloud service that provides an environment for running code associated with scholarly publications, and can be embedded in online journal articles. Currently in use by Cambridge University Press and Taylor & Francis
This workshop has three goals:
  • To showcase the state-of-the-art tools for writing computationally reproducible research. That is, how to write papers and reports in ways that include the computer code used to generate the results described in the document.
  • To provide hands-on tutorials in how researchers can use their tools in their own work
  • To collect feedback from researchers and look for opportunities for interoperability between the existing tools.
Tentative Schedule – Monday June 10th (OUG 220)
8:30 – 9:00AM – Registration Table Opens
9:15 – 10:00AM – Keynote presentation by Simine Vazire (Professor of Psychology at the University of California, Davis)
10:00 – 10:15AM – Morning tea (provided)
10:15 – 10:45AM – Lightning talks from UW researchers using executable notebooks
10:45 – 11:45AM – Presentation: High-level overview of Binder
11:45AM – 12:45PM – Presentation: High-level overview of Stencila
12:45 – 1:45PM – Lunch (provided)
1:45 – 2:45PM – Presentation: High-level overview of Whole Tale
2:45 – 3:00PM – Afternnon tea (provided)
3:00 – 4:00PM – Presentation: High level overview of Code Ocean
Tentative Schedule – Tuesday June 11th
9:00AM – 12:00PM (Rooms TBD) – Parallel in-depth tutorials
12:00 – 1:00PM – Lunch (provided)
1:00 – 3:00PM (OUG 220) – Panel discussion on common issues for tooling: interoperability, metadata for containers, archiving and persistent identifiers

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