Reproducible Documents
Realising reproducible documents with Texture and Stencila.

Adding reproducibility to the academic manuscript

Calls for transparency and reproducibility in science are becoming louder. Researchers want to share not only their final findings but also the underlying data and the methods used to generate the results.

In collaboration with eLife and Stencila, Substance is addressing this need by enabling reproducible elements in the Texture editor with the following goals in mind:

Source data
Source data is readily available in the publication and can be explored by the reader.
Code cells
Code cells allow live computations directly in the document authoring environment and reveal the scientific methods used.
Reproducible figures
The code and data used to generate a figure can be revealed and changed.

An open standard for representing reproducible research documents

The creation of open standard for exchange, submission and publication of reproducible documents is critically needed. Its widespread adoption within the academic publishing world would benefit the discoveries and persistence of research reported in this form. Substance in collaboration with Stencila meets this need by developing an extension to the DAR format. This will allow the data, code and computed outputs (graphs, statistical results, tables) embedded in a reproducible document to be recognised and presented online as an enhanced version of the published research article. In order to do this, we are representing these assets in JATS XML, the publishing standard through which research manuscripts are processed through the publishing workflow.

Stencila

Stencila is an open source platform, which provides easy-to-access computation environments for reproducible documents in the DAR format. Stencila makes reproducibility an integral part of a research publication (with live code execution) rather than attaching supplementary programming notebooks. Stencila is also capable of reading and writing existing well-established notebook formats such as Jupyter, RMarkdown etc.

Stencila in Texture

Substance is developing a Stencila plugin for Texture, which enables reproducible content types in the editor. It provides a seamless editing experience for both regular text and source code.