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BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

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Sunday, July 19 • 14:40 - 14:55
Executable Research Article (ERA): Enrich a research paper with code and data 🍐

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The presenter(s) will be available for live Q&A in this session (BCC West).

the eLife team and the Stencila team

(Presenter: Emmy Tsang, Innovation Community Manager, eLife; email: e.tsang@elifesciences.org)

Project Website: https://elifesci.org/reprodoc (this will be updated early June)
Source Code: https://github.com/stencila; https://github.com/elifesciences;
License: Apache License 2.0 (for Stencila); MIT (for eLife)

Main Text of Abstract

Code and data are important research output and integral to a full understanding of research
findings and experimental approaches in a paper. However, traditional research articles seldom
have these embedded in the manuscript's narrative, but instead, leave them as "supplementary
materials", if they are openly available.

With Executable Research Articles (ERAs), our vision is to enrich the traditional narrative of a
research article with code, data and interactive figures that can be executed in the browser,
downloaded and explored. It will give readers a direct insight into the methods, algorithms and key
data behind the published research.

We published our first demo ERA in February 2019. Over the past year, we have been working
closely with our collaborator Stencila to build an open tool stack that would enable our authors and
production team to easily publish ERAs at scale. In this talk, we hope to showcase the potential of
ERAs with examples and walk through how authors can enrich their traditional eLife paper using
Stencila Hub, through:

- Starting a Stencila Hub project linked to their eLife paper
- Converting the article to a reproducible notebook format of their preference, while preserving the relevant
 journal article metadata
- Uploading the data required to enable live re-execution of tables and figures in the article
- Replacing static tables and figures with code chunks that reproduce them

We will share our current vision of how ERAs will be integrated into our production workflow and
collect feedback. We also hope to engage participants in exploring potential functionalities for the
tool stack and building a community-driven roadmap.

avatar for Emmy Tsang

Emmy Tsang

Innovation Community Manager, Delft University of Technology

Sunday July 19, 2020 14:40 - 14:55 EDT