How to bring preprints to the charged field of medicine

“The founders of the popular biology preprint server bioRxiv have launched a repository on which medical scientists can share their results before peer review.

BioRxiv’s success prompted some clinical scientists to push for such a site because the biology repository accepts preprints in only certain fields of medical science. But some researchers are concerned that releasing unvetted clinical research could be risky, if patients or doctors act on what could end up being inaccurate information.

The organizations behind the new server, named medRxiv, have been working on the project since 2017 and say they have built in safeguards to address those concerns….”

Q&A: New Preprint Server for Clinical Research | The Scientist Magazine®

In general, there are a number of reasons. I think first and foremost it is speeding up dissemination of research. If you submit a paper to a journal, it takes on average about seven months before the work is actually published. But that’s an underestimate because normally a lot of times people have to go through various submission and rejection cycles at another journal. So it’s probably more like a year.

It’s not unheard of for people to spend two to three years waiting for the work to come out. And that’s all time where other people in the field could be reading it and building on that work. I think what’s important from a system-wide perspective, if you add up all those years, timesaving could be very important. Steve Quake of the Biohub did a back-of-the-envelope calculation. It could be that after 10 years you could speed up discovery five-fold.

From an individual’s point of view, if you’re a postdoc applying for tenure track, if you post a preprint, you can give to a hiring committee, tenure committee, or grant agency and say, ‘this is my most recent work,’ and show early evidence of productivity, rather than having to tread water for ages. This is particularly important for young scientists.

Finally, it’s an opportunity for authors to get feedback on their work from a very large number of people so that, when it is submitted for formal assessment by a journal, it’s in much better shape. . . . What’s happening there is a lot more people are looking at it than peer reviewers. Normally, you would have three people peer review a paper. If you put it on a preprint server, you could get feedback from, well, 4 million are looking at bioRxiveach month and not all of them are going to read all the papers, but way more than three will be looking at it….”

New preprint server for the health sciences announced today – Cold Spring Harbor Laboratory

Cold Spring Harbor Laboratory (CSHL), Yale University, and BMJ today announced the forthcoming launch of medRxiv (pronounced “med-archive”), a free online archive and distribution service for preprints in the medical and health sciences.

medRxiv is expected to begin accepting manuscripts on June 6th and will be overseen by the three organizations.

Preprints are preliminary versions of research articles that researchers share with each other before they are published in a journal, to enhance dissemination of study methods and findings among the scientific community and to solicit feedback to help improve the final published article….”

New preprint server for medical research | The BMJ

This debate is not new for The BMJ: over 20 years ago Tony Delamothe, the journal’s deputy editor, asked The BMJ’sreadership what we should do about electronic preprints,8 and the responses9 were similar to discussions now. The headline conclusion reached by Delamothe was that clear labelling of preprints might allow them to be used safely.8 As a result, BMJ launched the first clinical preprint server, ClinMedNetPrints.org, in 1999. The server operated until 2008 and received around 80 submissions before it was closed because of lack of use.

But times have changed, and we believe the need for an independent clinical preprint server remains. Clinical research can currently be found scattered on various preprint servers, ranging from bioRxiv and arXiv to servers established by publishers to link to their journals.10 We believe that the community will be served best by a preprint server that is specific to clinical research so that suitable safeguards can operate and by one that is not linked to specific journals or publishers but provides a central freely accessible archive.

BMJ (publisher of The BMJ) is therefore announcing its partnership with colleagues at Yale University and Cold Spring Harbor Laboratory to launch medRxiv. Harlan Krumholz and Joseph Ross, clinician-researchers at Yale, have long been advocates of preprints,4 while Cold Spring Harbor Laboratory operates the bioRxiv life sciences preprint server. BMJ brings its long experience of publishing and review of clinical research, researching the effects of changes in publishing,11 and publication ethics.12

In working to launch medRxiv we have focused on light-touch processes and workflows that we believe will reduce the potential for harm while retaining the advantages of speed and openness. A first step will be for authors to make various declarations about the work: how it has been conducted and reported, any conflicts of interest, and details of ethical approval. Then, all manuscripts will undergo several rapid rounds of screening before they are posted. The first will ensure that a manuscript is a research article (medRxiv will not accept case reports or opinion pieces, for example) and will cover obvious legal problems such as plagiarism and defamation. Then, a researcher in a relevant field will check the basic content and organisation of the article—but medRxiv does not endorse a manuscript’s methods, assumptions, conclusions, or scientific quality. And finally, a key screening question will be whether a preprint, if posted, has the potential to do harm to individual patients or the public. If in doubt medRxiv will not post the preprint; the authors will be encouraged instead to publish only after peer review.

By posting preprints, authors can help promote openness and transparency and reduce research waste from duplicated efforts and non-reporting. By helping ensure a balance of safety and speed, we believe medRxiv can provide a valuable service to the clinical research community. We will regularly report on any research that we do on the effect of preprints, and we encourage third parties to contact us for research opportunities. We also urge all readers of The BMJ and its sibling journals to read and deposit preprints in medRxiv. We look forward to reporting on its progress over the coming months….”

Free Machine Learning Repository Increases Accessibility in Genome Research | Technology Networks

Although the importance of machine learning methods in genome research has grown steadily in recent years, researchers have often had to resort to using obsolete software. Scientists in clinical research often did not have access to the most recent models. This will change with the new free open access repository: Kipoi.

Kipoi enables an easy exchange of machine learning models in the field of genome research. The repository was created by Julien Gagneur, Assistant Professor of Computational Biology at the TUM, in collaboration with researchers from the University of Cambridge, Stanford University, the European Bioinformatics Institute (EMBL-EBI) and the European Molecular Biology Laboratory (EMBL)….”

Surveying the landscape of products and services for sharing preprints – ASAPbio

“We are currently surveying the landscape of preprint servers and platforms and are aware of 15 different products or services in use or in development for sharing preprints. 

With over 1000 new corresponding authors now posting a preprint in the life sciences each month, the adoption of preprinting has been increasing rapidly. While the majority of the growth is currently driven by submissions to bioRxiv, which accepts preprints across the life and biomedical sciences, several preprint servers and platforms have launched in recent years to serve individual research areas and communities. Following developments in the landscape over the past two years, preprint server operators now have a range of products and services to choose between. Today, we share a listing of the preprint server products and services known to ASAPbio. We welcome feedback and information from product owners, service operators and preprint server owners to grow and improve this independent listing….”

What bioRxiv’s first 30,000 preprints reveal about biologists

“Researchers posted more preprints to the bioRxiv server in 2018 alone than in the four previous years, according to an analysis of the 37,648 preprints posted on the site in its first 5 years.

The analysis also shows that the number of downloads from the site has topped 1 million per month. BioRxiv, which allows researchers in the life sciences to post preliminary versions of studies, turned five last November….

Preprints that are downloaded more often on bioRxiv tend to be published in journals with higher impact factors than preprints that are not downloaded as much….”

arXiv Update – January 2019 – arXiv public wiki – Dashboard

“In 2018, the repository received 140,616 new submissions, a 14% increase from 2017. The subject distribution is evolving as Computer Science represented about 26% of overall submissions, and Math 24%. There were about 228 million downloads from all over the world. arXiv is truly a global resource, with almost 90% of supporting funds coming from sources other than Cornell and 70% of institutional use coming from countries other than the U.S….”