Open-Source Community Call: Exploring tools for reproducible research

Community members share the latest efforts and opportunities in developing tools for conducting and communicating research.
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During the community call that took place in the last week of June, seven presenters shared updates on their work, including the latest news from the Chan Zuckerberg Initiative (CZI), Binder, Manuscripts.io and more.

Emmy Tsang (Innovation Community Manager) shared eLife’s latest plans to develop a scalable solution for the authoring and publishing of reproducible articles. As part of the Reproducible Document Stack (RDS) project, Stencila is building Encoda, a tool to convert from multiple existing formats like Jupyter Notebooks and R markdowns to DAR, and Dockta, for building optimised Docker images.

Dario Taraborelli from CZI presented the “Essential Open Source Software for Science” programme. CZI invites applications from open-source software essential to biomedical research, and applicants can request funding between $50k and $250k for one year. The first round of applications, the first of three distinct cycles, is open now until Aug 1, 2019.

Diego Arenas from the Alan Turing Institute introduced Machine Learning in Julia (MLJ). Julia, a programming language, combines the simplicity of Python and speed of C++. The project’s aim is to accelerate deployment by developing a machine-learning toolbox for Julia, such that researchers and engineers can work on a single, shared and refined code base.

Matthew Conlen from the University of Washington presented Idyll, a markup language for the authoring and publishing of interactive narratives. Idyll implements a flexible article model, giving authors control over document style and layout, reader-driven events (such as button clicks and scroll triggers), and a structured interface to JavaScript components. Recent extensions automate the detailed instrumentation of interactive articles and corresponding visual analysis tools for inspecting reader behaviours.

Chris Holdgraf from the University of California, Berkeley, and Project Jupyter gave an exciting update on BinderHub. A technology stack to build and serve binders, BinderHubs is now officially out of beta, while BinderHubs are being deployed all around the world. Having secured a second host cluster, mybinder.org is now a federation and is looking for more hosts to help share the load. In addition, Binder links can now point to Zenodo repositories. The Binder team is interested in plugging further tools and platforms into the Jupyter/Binder ecosystem.

Alf Eaton shared the latest developments of Manuscripts.io, an open-source tool for collaboratively writing complex documents. Manuscripts.io now serves document-style templates from multiple common journals, and users are invited to try it out in-browser.

Dav Clark discussed Gigantum’s approach to facilitating reproducible research. Gigantum is based on an MIT-licensed client that runs in a Docker container to automate versioning, environments, collaboration and containerisation. Dav highlighted the need for a broader conversation on reproducibility, to review community needs and to consolidate future development directions.

We hope to hear from Stian Soiland-Reyes on the Research Object Crate project in our next open-source community call, which will take place in October 2019. If you’d also like to present your work then, please get in touch with us on innovation [at] elifesciences.org or @eLifeInnovation on Twitter – the community will be interested to hear about your open-source tool for improving the way science is communicated.

Full notes from the June call, including questions and comments that were made in writing only during and/or directly after the meeting, are available here: https://public.etherpad-mozilla.org/p/community-call-Jun24-2019

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