[Bioc-devel] eLife supports development of open technology stack for publishing reproducible manuscripts online

Emily Packer e.packer at elifesciences.org
Thu Sep 7 18:12:17 CEST 2017

Hi all,

I thought you might be interested in our announcement that eLife, in
collaboration with Substance and Stencila, is supporting a project to
create a full, open technology stack for authoring, compiling and
publishing computationally reproducible manuscripts online.

Currently, researchers are able to document their computational experiments
through file formats such as R Markdown and platforms such as Jupyter.
However, there is no means for a researcher to present their research in
this form through the traditional journal. Instead, current users of these
technologies submit a “flattened” version of the documents to a journal,
losing the value of embedded code and data references.

Offering a means to share reproducible documents through an open stack of
tools for authoring, compiling and publishing computationally reproducible
manuscripts online would help counter this challenge and incentivise the
sharing of reusable data and code underlying a research article. To help
address this need, eLife is supporting the development of such a
Reproducible Document Stack, in collaboration with Substance and Stencila.

As part of this project, we aim to add several extensions to JATS XML that
enable reproducible elements, such as statistical results, tables or
graphs, to be embedded within journal articles. These extensions will allow
such reproducible elements to be preserved right through the authoring,
review and production pipeline. Ultimately, we hope the project will
the sharing of demonstrably reusable data and code underlying a research

Please see the full announcement for more information:

You can also read more about the Reproducible Document Stack in our
accompanying eLife Labs post:

If you’d like any further information at all, please don’t hesitate to
contact me.

Best wishes,



*eLife's early-career researcher travel grants 2017 are now open for
Visit https://elifesciences.org/elife-news/inside-elife-2017-travel-grants-early-career-researchers-now-open-applications

Emily Packer
Press Officer

+44 1223 855373 (office)


eLife Sciences Publications, Ltd is a limited liability non-profit
non-stock corporation incorporated in the State of Delaware, USA, with
company number 5030732, and is registered in the UK with company number
FC030576 and branch number BR015634 at the address First Floor, 24 Hills
Road, Cambridge CB2 1JP.

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