Q&A with Dr. John Inglis, co-founder of bioRxiv and medRxiv, and Executive Director of Cold Spring Harbor Laboratory Press

The use of biology pre-prints has taken off in a huge way. In a previous article (bioRxiv: give pre-prints a chance) we spoke to scientists who had nothing but good things to say about their experiences of using the original biology pre-print server, bioRxiv. Their overall opinion was that using pre-prints increased the visibility of their work, enabled quick feedback from the community, and gave a feeling of accomplishment, without months of painful peer-review. To find out more about the overall success of biology pre-prints we caught up with the co-founder of bioRxiv (and more recently, medRxiv), Dr. John Inglis, to discuss the pre-print revolution and what he believes is yet to come for the future of science publishing.

What’s your background? Have you always been deep in the world of academia?

I did a PhD at Edinburgh University Medical School and then had the great good fortune to be taken on by The Lancet in London as an Assistant Editor. Three years later, I was offered the chance to join a small outpost of the Elsevier empire in Cambridge where the Trends monthly review journals were published. I was the founding editor of Immunology Today, then created Parasitology Today (both later renamed as Trends journals) and eventually managed a number of the journals.

Seven years later, Jim Watson, Director of Cold Spring Harbor Laboratory in New York, approached me about coming to the Laboratory “for a year or two” to take over the small but influential book publishing operation that a few months earlier had added a journal, Genes & Development. I founded Cold Spring Harbor Laboratory Press the following year and now, 30 years later, it has 9 journals and 200 books in print and electronic form.

What was it that drove you to set up bioRxiv? What made you finally say, “enough is enough, biological science needs a preprint server too!”

The advent of digital publishing in the mid-1990s brought together organizations and research communities that didn’t know much about each other’s cultures and information habits. So, through meetings like the National Academy’s Electronic Publishing Summits, those of us in biomedical publishing became aware of arXiv, the preprint server that was at the center of the information universe for physicists and mathematicians but operated in a way that simply didn’t seem feasible for other scientific disciplines. And that impression was borne out by the failure of efforts by several publishers in the late 90s and early 2000s to establish preprint servers for biology and medicine.

we developed a hunch that it was an opportune time to make another attempt at a preprint server for biology

My colleague, Richard Sever, and I were aware of this history. But by being at Cold Spring Harbor Laboratory, home of the most important annual meeting in genomics and publisher of the journal Genome Research, we had the chance to talk to many genome scientists whose attitudes to sharing research and data had been much influenced by the collegial and collaborative nature of the Human Genome Project. And also to an influx of new faculty members in quantitative biology at the Laboratory whose backgrounds were in physics and math and who asked, “where is the arXiv for biology?”.

So, we developed a hunch that it was an opportune time to make another attempt at a preprint server for biology, and with its 100-year history as a place where scientists came to share their work in person, the Laboratory seemed to be a natural home for an online information-sharing initiative. The President, Bruce Stillman, was a strong supporter from the start and was willing to provide startup funding. bioRxiv launched in November 2013.

How is bioRxiv doing now? You recently celebrated the 50,000th posted pre-print. Can you give us some more numbers to show how popular bioRxiv has become?

The server currently has 56,000 original submissions, with 20,000 revised versions, from 230,000 authors in 19,000 institutions in 110 countries. The rate of new submissions keeps climbing and last month (July 2019) we received the largest monthly total ever, over 2,600 papers, with nearly 1,000 revisions. The usage of the site is also rising fast and each month we now see over 5 million abstract page views and PDF downloads. Thanks to generous financial support from the Chan Zuckerberg Initiative, we have been able to convert all the bioRxiv manuscripts into XML so that every paper can now be read online without downloading, and the usage of the full text online is also rising steeply.

Over 70% of papers posted to bioRxiv are published within two years

The conversation around individual preprints takes place in part privately (email, conversations at conferences) but also increasingly in public, through hundreds of thousands of tweets, moderated comments on the site (more than 6000), and preprint evaluation initiatives like PREreview, preLights, and Peer Community. Over 70% of papers posted to bioRxiv are published within two years and there have been several recent studies suggesting that papers with preprint versions are cited more often and have higher attention scores than papers without a preprint.

Can you tell us a bit about medRxiv? What are the key differences between this and bioRxiv?

Two years into bioRxiv’s development, two innovative physicians, Harlan Krumholz and Eric Topol, published an op-ed in The New York Timessaying that medicine needed the equivalent of bioRxiv. In response, we added to bioRxiv two clinically oriented subject categories, Clinical Trials and Epidemiology, as a pilot to see what the response would be. It was encouraging and we decided to embark on the creation of a separate server for health sciences. It had to be separate from bioRxiv because the risks in sharing non-peer-reviewed medical information, we felt, should be mitigated by placing specific requirements on medRxiv authors and taking special care in screening submissions.

The bioRxiv team celebrating the launch of medRxiv. From left to right; Jan Argentine (Screening Lead), John Inglis (Co-founder), Linda Sussman (Director of Publication Services), Ted Roeder (Lead Developer), Richard Sever (Co-founder), Sam Hindle (Content Lead), Inset: Kevin-John Black (Product Lead).

medRxiv has been created in close collaboration with Yale University and the London-based global health knowledge provider BMJ and is managed by a team consisting of two Yale professors of medicine, Harlan Krumholz and Joe Ross, two senior BMJ staff members, Theo Bloom and Claire Rawlinson, and Richard Sever and myself from Cold Spring Harbor. Together we’ve established the declarations that authors must make when submitting papers (eg approval by IRBs, conflict of interest disclosure, clinical trial registration, data availability statement). And if the screening team concludes that a paper presents information that might lead to potentially risky changes in health-related behavior or in how patients are treated, we reserve the right to suggest that it is more suitable for dissemination after peer review than as a preprint. One month after medRxiv was launched it had 150 papers, a much faster start than we saw with bioRxiv.

Will more pre-print servers be springing up?

Until 2013, the world of preprints was largely restricted to arXiv, the Social Science Research Network, the French language preprint repository HAL, and some others. Since 2013, there has been a proliferation of preprint servers, many focused on specific areas of research like psychology, social science, chemistry, and earth science, and some on the scientific output of specific countries or regions like India, Africa, or Indonesia, or in certain languages like French or Arabic. At my last count, there were at least 45 preprint repositories and yes, I’m sure there will be more.

Can you talk a bit about Springer-Nature’s updated policy to encourage pre-print sharing? What does this mean for the future of bioRxiv?

One of the chief reasons a scientist might hesitate about posting a preprint is anxiety that they won’t be able to publish their paper where they want to because the journal concerned regards a preprint as prior publication. General journals like Science, Nature, and PNAS came to terms with this years ago because they handled submissions that began life as arXiv preprints. But many biomedical journals had not had this experience when bioRxiv began. Nevertheless, a number of journals, especially those owned by scholarly societies, quickly announced their receptivity to preprint submission.

bioRxiv offers authors the chance to submit their paper directly to a journal for editorial consideration and there are currently over 140 journals for authors to choose from. So, we are deeply grateful to all the many journals and publishers that have clarified or modified their policies to reassure authors that they would welcome preprint submissions. We are aware that there is still work to do in this area, particularly with publications in emerging research communities internationally.

What do you think the future will bring for pre-prints? Is there even the slightest possibility that the subscription model for science will go in the bin, and open access will be the default? Especially considering the momentum Plan S is building.

Many preprint repositories are new and not well resourced, and it is too early to judge whether their communities have embraced them. This kind of growth takes time and I think it is very unlikely that preprints per se will drive the subscription model into the bin. But the popularity of preprints in more and more fields is symptomatic of a growing community desire for greater and more immediate access to recent research.

Plan S seems often to be less about universal access and more about forcing a change in the business model of journal publishing

The debate about whether APC-based open access (OA) journal publishing is the golden road to open science has been long and contentious. That model is progressing towards being the default for certain fields where it’s culturally appropriate and there are available funds to support it. But if the aim is to provide universal access to research, Richard Sever, Mike Eisen (Editor-in-Chief of eLife), and I argued in a recent paper that it could be accomplished simply and relatively cheaply if all research funders just mandated the posting of preprints by all the investigators they support. We called this Plan U. Plan S seems often to be less about universal access and more about forcing a change in the business model of journal publishing.

It seems like bioRxiv is more popular in some areas, ie bioinformatics and genomics than it is others. Can you comment on the variation in its popularity between research areas?

once a community embraces preprints, it never goes back

The largest subject category on bioRxiv is neuroscience, with bioinformatics and genomics 2nd and 3rd. This distribution is influenced by the enormous size of the neuroscience research community. I have no data but it’s my impression that in certain fields like genomics, posting preprints has become – as a young postdoc with a poster presentation at a recent Cold Spring Harbor meeting told me – a moral obligation. Different fields have different cultures, different demographics (different proportions of conservative, often older influencers who don’t read or post preprints), and different ways of communicating (for example in their use of Twitter). The arXiv first took root in high energy physics, then its influence percolated through other areas of the discipline and continues to do so. arXiv’s founder, Paul Ginsparg, has observed that once a community embraces preprints, it never goes back. My guess is that we are seeing the same process at work in biomedical science.

Is there any journal rivalry? How do the subscription model journals feel about you guys and your open access model?

We have tracked bioRxiv preprints into more than 2,000 journals and they vary enormously in their scope

bioRxiv would not have been able to establish itself if journals en masse had decided not to consider manuscripts that had been posted as preprints. One or two publishing organizations did take that position when bioRxiv began but changed it under community pressure. We made many efforts to get across the fact that bioRxiv was not hostile to journals, was not a tool to enable a particular publisher to gain an advantage, and that we aimed to insert bioRxiv into an information ecosystem in which journals continue to do the vital work of peer review. We have tracked bioRxiv preprints into more than 2,000 journals and they vary enormously in their scope (from the general to the highly specialized), their prominence, and their business models (subscriptions, hybrids, gold OA, diamond OA). So, we feel we are making progress in that integration process.

Where do you personally want science publishing – or just the communication of scientists’ research – to end up?

I believe bioRxiv has shown the power and benefits of decoupling the dissemination of recent research results from their evaluation. The community has free access to these results and experts can use preprints critically to guide their own studies and accelerate the pace of research. Authors get the benefit of a large and diverse audience of readers and have the opportunity to hear from them and improve their manuscript before submitting for publication. Freed from the need to disseminate the information in a paper for the first time, journals can focus instead on the processes of evaluating the content through peer review, curating the material they deem important, and illuminating and putting in context these important results for those who aren’t experts.

science publishing is finally embracing the possibilities of network technologies

There is an appetite for change along these lines and at bioRxiv, we are embarking on a pilot with a group of journals interested in exploring the possibilities. I don’t know where any of this will end up, or if indeed it will “end” anywhere any time soon. We are still at the beginning of a period of extraordinarily interesting change in which science publishing is finally embracing the possibilities of network technologies. It is fascinating to observe, and I am very privileged to have a small part to play.

Preprints are clearly in an incredibly exciting place and biological science seems poised to take what could be a momentous shift in the way research is shared and consumed. We love everything about the open scientific communities that preprints foster and cannot wait to see how this story unfolds. But where do you stand on preprints? Have you had the opportunity to share your work through a pre-print server like bioRxiv? Get in touch with us on social and share your thoughts on the pre-print revolution.