Section 1 Introduction

1.1 Literate Science

A new paradigm for academic publishing

This is currently very much a work in progress and may change dramatically and rapidly, some sections may be drafts, outlines and bullet points to be filled in and properly edited as I go

This is an outline for a new academic publishing paradigm with reforms spanning the types of article we publish, the formats in which we author them and the business models of publishers. These proposals aim to address a number of the systemic issues by which academic publishing is currently beset. They range from the seemingly minor impracticalities associated with submitting papers through to the extractive business practices of a number of large incumbent publishers, the vicissitudes of peer-review, irreproducible analyses, the form and function of papers and a number of other issues.

These proposals draw on ideas from previous ‘unconventional’ publication platforms such as f-1000, peerj, elife (particularly their libero publishing suite), JoVE - journal of visualised experiments, and microPublication. They also draw from RopenSci’s software review process and Journal of open source software JOSS, indeed extensive inspiration is drawn from the free & open source software communities more generally. In addition they draw from the ideas of nano-publications and single observation publishing from ScienceMatters/EUREKA,1 as well as community contributions to shared protocols and pipelines from protocols.io2 and nf-core.

Furthermore a number of tools, ideas and practices from modern software development contribute to the bases of some of the proposals to follow. These include: The concept of literate programming in which code and it’s documentation, context and explanation are part of the same corpus of text. Version/source control of text with git facilitating distributed collaboration on texts, history and tracking of changes, and attribution of authorship of individual contributions to a text. Reproducible computational environments with containerization technologies such as docker and Continuous integration/deployment pipelines to automate testing, checking and building and deployment/publication of software products. Platforms such as Renku which facilitate the use of these tools including gitlab together in an integrated platform.

The economics and game theory of proposed solutions as well as gaining the trust and confidence of the academic community are given central importance here and the technical considerations are a means to this end.

What I describe here aspires to be a unified vision for bringing together a number of different reforms, you may disagree with my analysis and/or proposed solutions for a particular problem or even that something that I point to as a problem is one. Whilst I think the separate elements of this fit together into a cohesive whole I would urge the reader to consider the merits of the specific proposals separately as I think some are individually valuable.

I welcome critique and feedback on all of this content. This document is published as a ‘git-book’ using bookdown (Xie 2020) if you would like to discuss it’s content please do so in the discussion section associated with git repository on github if you have a specific problem, fact check or correction please open an issue, if you would like to suggest an edit, and are willing to specify the exact changes you’d like to see made please open a pull request.

References

Xie, Yihui. 2020. Bookdown: Authoring Books and Technical Documents with R Markdown. https://github.com/rstudio/bookdown.

  1. Now defunct? Dead links https://www.reddit.com/r/TokenEUREKA/, https://doi.org/10.1038/d41586-019-00447-9, https://medium.com/eureka-token/stories-can-wait-science-cant-33810dd17c9f↩︎

  2. GPL like agreement for lab protocols? Copy the obligation to make changes available to the upstream, and encourage upstreaming them yourself by publishing your protocols under the same licence. If you use a protocol and cite it you must describe your modifications to it and release them under the same terms as the original. enforcibility? comercial incentives might limit adoption due to regressive attitudes to IP control rather than emphasis on convenience and quality of service↩︎