Everything Hertz: 122: Reoptimizing scientific publishing for the internet age (with Michael Eisen)

“The internet should have transformed science publishing, but it didn’t. We chat with Michael Eisen (Editor-in-Chief of eLife) about reoptimizing scientific publishing and peer review for the internet age.

Here what we cover and some links:

How Michael co-founded PLOS
The book Dan mentioned on the history of the scientific journal
Why did eLife launch? What did it offer that other journals didn’t?
Nature’s recently proposed $11k article processing fee proposal
eLife’s new “author-driven publishing” approach, in which all submitted papers have to be posted as preprints
Part two of our conversation will be released on January 4, 2021 …”

Open-access journal eLife announces ‘preprint first’ publishing model

“The open-access journal eLife has unveiled plans to introduce a new publishing model. Starting next July, the journal will adopt a “publish, then review” policy, and will make all of its peer-review reports publicly available.

Under the policy, which the journal announced1 on 1 December, eLife will only review and publish papers that have already been posted on a preprint server, such as bioRxiv, medRxiv or arXiv. Submitted papers that aren’t already on preprint servers will be posted on bioRxiv or medRxiv….”

Gobsmacked

“You have to hand it to Springer Nature: they really are trying. Beset, as are all publishers with traditional business models, with challenges concerning open access (OA) from libraries, funders, and authors, SN is attempting to win the prize for Most Cooperative Publisher. This is not purely a recent development; Springer acquired OA pioneer BioMed Central way back in 2008 (it did not merge with the Nature Publishing Group until 2015). It has negotiated numerous “transformative” agreements with various national consortia and funding bodies and appears to have even come to terms with cOAlition S, a populist, authoritarian organization that is attempting to foment a worldwide revolution. (We note in passing that we are always a bit skeptical about organizations that fail to capitalize the first letter of a proper noun.) Until now, however, SN was not working to transform the models of its top-tier journals, usually holding the journals in its Nature portfolio out of comprehensive OA agreements. But that has started to change as evidenced by the announcements of both a new transformative deal with Max Planck and a new OA program whereby authors (or the funders of their work) can now pay to publish (Gold OA) in Nature and certain other journals in the Nature-branded portfolio. Whether this program proves to be successful (and whether the transformative deal with Max Planck proves extensible to other organizations) or not is a critical test of the ability of the company, and the industry at large, to accommodate the growing demands of funders and (mostly European) consortia with the prestige economy of academic research, where Nature sits at the very apex….

It is not only cOAlition S that SN must make happy, alas. Of primary concern to the management, not to mention the owners, is liquidity: how can some portion of the SN asset be converted into cash? SN has tried and failed, tried and failed again to go public. Part of the reason is that the OA business looks to investors like a model that is not ultimately as remunerative as the subscription model it is replacing. Convincing investors that they have figured out an OA long game is therefore essential. If investors do not believe in the strategy, SN may never fetch the price its current owners hope for (and that their creditors demand). What makes this complicated is that investors in Frankfurt and on Wall Street sit on one side of SN’s aspirations and on the other sits a community-anchored movement, many of whose members are characteristically suspicious of capitalism. …”

Nature’s New Open Access Option: A Dinosaur Lurches Toward the Future

“Nature has introduced a new Open Access Options. It is suggested that this strategy will be ineffective. Rather, it is suggested that the strategy of post publication review proposed by eLife is a better route to a open future for scholarly communication.”

In biology publishing shakeup, eLife will require submissions to be posted as preprints | Science | AAAS

“When major biomedical research funders launched the open-access journal eLife in 2012, they hoped it would push biomedical publishing to take full advantage of the internet’s power to share results freely and instantly. In the ensuing years, the open-access model has caught on. And more and more biologists have shared work in online preprint servers such as bioRxiv and medRxiv before undergoing peer review.

But those changes are not enough for Michael Eisen, a biologist at the University of California, Berkeley, and the journal’s editor-in-chief since 2019. This week, eLife announced it will only review manuscripts that have been posted as preprints. And all peer reviews will be made public, including those for manuscripts the journal rejects. Eisen sees the changes as the next logical step in the evolution of the preprint, he told ScienceInsider….”

eLife shifting to exclusively reviewing preprints | For the press | eLife

“eLife has announced that it is transitioning to a new ‘publish, then review’ model for science publishing, in which the journal will exclusively review preprints and its editors and reviewers will focus on producing high-quality peer reviews that will be made public alongside the preprints.

These steps advance eLife’s mission of transforming the communication of new biology and medicine research, and come amid increasing support for preprints within the life science community, including eLife authors. A recent internal analysis showed that around 70% of papers under review at eLife were already available as preprints. The organisation began trialing this system with Preprint Review – an opt-in service for reviewing preprints posted on bioRxiv, which has seen more than 250 papers reviewed since its launch in May….”

ANN: A platform to annotate text with Wikidata IDs | Zenodo

Abstract:  Report of the work done by the Ann team at the eLife Sprint 2020. 

It describes the effort pursued towards a system for universal annotation of biomedical articles using the collaborative knowledge graph of Wikidata.  

The project is currently active at https://github.com/lubianat/ann. 

A web-native approach to open source scientific publishing | Opensource.com

“This summer, eLife was pleased to launch Executable Research Articles (ERAs) in partnership with Stencila, allowing authors to post computationally reproducible versions of their published papers in the open-access journal.

The open source ERA technology stack delivers a truly web-native format that treats live, interactive code as a first-class asset. It was developed to address current challenges around reproducing and reusing published results—challenges mostly caused by the lack of infrastructure for publishers to showcase the richness and sophistication of the computational methods used by researchers in their work.

As part of its mission to transform research communication, eLife invests in open source technology innovation to modernize the infrastructure for science publishing and improve online tools for sharing, using, and interacting with new results. The organization began work on the concept of computationally reproducible papers in 2017, first in partnership with Substance and later, with Stencila, and announced a number of milestones along the road to delivering ERA….”

A web-native approach to open source scientific publishing | Opensource.com

“This summer, eLife was pleased to launch Executable Research Articles (ERAs) in partnership with Stencila, allowing authors to post computationally reproducible versions of their published papers in the open-access journal.

The open source ERA technology stack delivers a truly web-native format that treats live, interactive code as a first-class asset. It was developed to address current challenges around reproducing and reusing published results—challenges mostly caused by the lack of infrastructure for publishers to showcase the richness and sophistication of the computational methods used by researchers in their work.

As part of its mission to transform research communication, eLife invests in open source technology innovation to modernize the infrastructure for science publishing and improve online tools for sharing, using, and interacting with new results. The organization began work on the concept of computationally reproducible papers in 2017, first in partnership with Substance and later, with Stencila, and announced a number of milestones along the road to delivering ERA….”

Affordabee: Low-Cost Open Access Publishing – eLife Innovation Sprint 2020

“Adam is an MSc student at a local university in Kenya. He has to work part time to pay his school fees. Adam does the same through his research project to pay for bench fees at a local research institution. Through sweat and long nights, he manages to get a manuscript ready, as he has to publish to graduate. Adam recently attended a seminar where he was introduced to open science. He is excited about his first paper and wants to publish open access. His excitement is cut short when he realises he has to pay a US$3,000 article processing charge (APC) to get his manuscript published. What are his options? Are there publishers that can offer him a waiver or a subsidy? Or, are there some funding opportunities he can tap into for support?

We envision a platform that can help Adam identify journals that can offer him waivers or subsidies, and how to access them; a platform that will point him to funding opportunities to help cover the APC. We seek a platform that will reduce the APC cost barrier for students from resource-poor settings, like Adam. …”

Preprints & COVID-19 • covidpreprints

“The database is being actively maintiained & managed by Zhang-He Goh (@zhanghe_goh), Gautam Dey (@Dey_Gautam) & Jonny Coates (@JACoates91). For any queries or questions please contact Jonny at jonathon.coates@qmul.ac.uk or preLights at prelights@biologists.com

In addition, our thanks go out to the wider scientific community who are diligently assessing and communicating important preprints during this difficult time.

preLights is a community service supported by The Company of Biologists, the not-for-profit publisher of Development, Journal of Cell Science, Journal of Experimental Biology, Disease Models & Mechanisms and Biology Open. The Company of Biologists is also a UK charity, providing grants and other support for the scientific community. …”

Register Now for Open Source Community Call – Sept 2020 | FORCE11

“Join the Open Source Community Call co-hosted by FORCE11, Dryad, and eLife on September 29th, 3pm UTC (8am PDT, 11am EDT, 4pm BST)

Innovators share the latest updates and opportunities in the open-source space for research communication and publishing. Representatives from open source projects present in a ‘lightning talk’ format, 5 minutes or less, to share about projects and communities that are emerging or underway, so we can learn more about available open resources, where we can engage or contribute and consider where collaboration can contribute to the path forward….”

Welcome to a new ERA of reproducible publishing | Labs | eLife

“Since 2017, we have been working on the concept of computationally reproducible papers. The open-source suite of tools that started life as the Reproducible Document Stack is now live on eLife as ERA, the Executable Research Article, delivering a truly web-native format for taking published research to a new level of transparency, reproducibility and interactivity.

From today, authors with a published eLife paper can register their interest to enrich their published work with the addition of live code blocks, programmatically-generated interactive figures, and dynamically generated in-line values, using familiar tools like R Markdown and Jupyter in combination with Stencila Hub’s intuitive asset management and format conversion interface. The resulting new ERA publication will be presented as a complement to the original published paper. Very soon, a Google Docs plugin will also be made available to let authors insert executable code and data blocks into their documents using the cloud service.

Readers of ERA publications will be able to inspect the code, modify it, and re-execute it directly in the browser, enabling them to better understand how a figure is generated. They will be able to change a plot from one format to another, alter the data range of a specific analysis, and much more. All changes are limited to an individual’s browsing session and do not affect the published article, so anyone can experiment safely. Readers can also download the ERA publication – with all embedded code and data preserved – and use it as a basis for further study or derivative works….”