We've been working on a proposal for representing reproducible publications as a bundle of accessible files (manuscript + data sheets + static assets). This format relies on existing standards where possible (e.g. JATS for representing manuscripts) and is designed to be a submission format publishers accept (our partner eLife to be the first one). That way authors are able to create a standardised reproducible publication in Stencila (or a similar tool) and submit to a publisher as is, without limitations.
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Thank you for your help!