Writing Reproducible and Executable Scientific Papers with R & Python

The eScience Institute empowers researchers and students in all fields to answer fundamental questions through the use of large, complex, and noisy data. As the hub of data-intensive discovery on campus, we lead a community of innovators in the techniques, technologies, and best practices of data science and the fields that depend on them.Specifically, we:1.Bring expertise and help researchers at UW to leverage data science tools, methods, and best practices in their research and in their grant proposals.2.Are data science experts and, in collaboration with faculty at UW, advance the state-of-the-art in data science methods and in domain sciences that benefit from them.

University of Washington eScience Institute

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:
<UL>
<LI>
<A HREF="https://mybinder.org/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">Binder</A> 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. 
</LI>
<LI>
<A HREF="http://stenci.la/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">Stencila</A> 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. 
</LI>
<LI>
<A HREF="http://wholetale.org/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">Whole Tale</A> 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 <A HREF="https://www.dataone.org/current-member-nodes" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">DataONE member nodes</A>. 
</LI>
<LI>
<A HREF="https://codeocean.com/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">Code Ocean</A> 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. 
</LI>
</UL>
This workshop has three goals:
<UL>
<LI>
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. 
</LI>
<LI>
To provide hands-on tutorials in how researchers can use their tools in their own work
</LI>
<LI>
To collect feedback from researchers and look for opportunities for interoperability between the existing tools.
</LI>
</UL>
 
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 <A HREF="https://escience.washington.edu/about-us/visit-us/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">eScience Institute</A> 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
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<IMG ALT="logos" SRC="https://cdn.evbuc.com/eventlogos/174908558/reproducibilitycollage2.png">
<IMG ALT="Code-Ocean-logo" SRC="https://assets-global.website-files.com/586cc078fcd66fc24dc054b4/5c5bfa997ebe992af69eefc6_Endless%20Horizental%20Negative.svg">

Odegaard Undergraduate Library (OUGL) 220

Thank you for registering to attend the Writing Reproducible and Executable Scientific Papers workshop! We look forward to seeing you in June.

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Writing Reproducible and Executable Scientific Papers with R & Python

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