Scientific publishing is undergoing a transition from corporate-controlled, for-profit publishing to more open models. While “Open-Access”, is part of this, there are a number of considerations important in true “Open Publishing”:

  1. Free access to the public (who pays for most of the research via their taxes!)
  2. Free submission of articles by authors
  3. Open Data - where original data and analysis workflows are made public
  4. Creative Commons - otherwise known as Copyleft, where rights are retained by the author but the content is usable with attribution
  5. Transparency of the review process (with or without anonymity)
  6. Open software, standards and tools used in the publication process

This post will focus on item (6) from above. While the choice of software tools is rarely considered as part of the Open Publishing ecosystem, it is of key importance. The economics of publishing are highly dependent on software. Open-source software enables the creation of open journals. This post will be followed-up with some discussion in the frture about how Open Publishing systems can be structured with incentives aligned to the best interests of the progress of science.

An overview

Scientific publishing software usually involves a supported workflow with four main components:

  1. submission
  2. review and communication
  3. editing and formatting
  4. publication

It could be argued that other functions are also part of this workflow (raw data archiving for instance), but let’s just explore core functionality for the moment. Open-source publication systems are usually web-based and facilitate the workflow by guiding authors, reviewers and editors. The following is a table of all the currently supported open publishing systems I could find (please let me know if you find others).

Name/link Organisation Language License LaTeX Notes
Open Journal Systems Public Knowledge Project used by PsychOpen Journals
DPubS Cornell University Perl/Java
ePublishing Toolkit Python Yes Mostly offline tools
Ambra PLOS Java MIT Used to publish PLOS journals, mostly developed for internal use
Janeway Birkbeck, University of London Python AGPL3 No Modern and well documented
Coko xPub Collaborative Knowledge Foundation Node.js MIT Designed for web-based editing with PubSweet
Libero Python

It’s an interesting list, with some new and some old software stacks evident. Over the next few months I will try installing some of these packages. The ones that have stood out so far are:

I’d like to try Ambra but it looks poorly documented and probably too heavy for a test install. The other platforms all seem a bit specialised. I’d love to see an RMarkdown based journal workflow, who knows, one of the above may be extensible to that format, that’s the best thing about open-source!

Some extensions on basic features

Web Editing

In the future, review systems will allow in-place web editing. This is somewhat new and only a few platforms have emerged. Eventually they will need better integration into publishing platforms:


Rich Review

In addition to commenting, it is likely that the review cycle will become more fine-grained and peer-sourced.