Writing reproducible & executable scientific papers with R & Python: A hands-on eScience workshop

Overview

This workshop is the signature event of the UW eScience Special Interest Group on Reproducible Research and Open Source Software, co-sponsored by the UW Libraries. Our 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. The Binder workshop will be most relevant for researchers who already use code sharing services, such as GitHub, to share and collaborate on Python and R code.
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. The Stencila workshop will best suited to researchers who prefer intuitive word processor and spreadsheet interfaces, and want to work more reproducibly in these environments.
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. The Whole Tale workshop is best for researchers who use Jupyter notebooks or RStudio and who routinely deposit or use data that are deposited on repositories such as Dataverse, Dryad, USGS or other DataONE member nodes.
Code Ocean with Seth Green: an in-browser cloud service that provides an environment for running code associated with scholarly publications, and embedding that code in online journal articles. Currently in use by Cambridge University Press and Taylor & Francis. The Code Ocean workshop will be most relevant to researchers are curious about how to embed executable code in their next journal article.

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.

Schedule

Monday June 10th (OUG 220)

8:30-9:00am - Registration Table Opens

9:00-9:15am - Welcome and Introduction by Ben Marwick

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

Tuesday June 11th

8:45am - Meet in the eScience Institute to walk to breakout rooms, 6th floor Physics/Astronomy Tower

9:00am - 12:00pm (Rooms TBD) - Parallel in-depth tutorials for Binder, Stencila, Whole Tale, Code Ocean

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

Logos

logos

Code-Ocean-logo

Registrations are closed

Writing Reproducible and Executable Scientific Papers with R & Python