Category Archives: News

Vale & Hyman publish eLife article on preprints & priority

Tony Hyman and ASAPbio founder Ron Vale have just published a Point of View in eLife building on their earlier blog post.

ABSTRACT: The job of a scientist is to make a discovery and then communicate this new knowledge to others. For a scientist to be successful, he or she needs to be able to claim credit or priority for discoveries throughout their career. However, despite being fundamental to the reward system of science, the principles for establishing the “priority of discovery” are rarely discussed. Here we break down priority into two steps: disclosure, in which the discovery is released to the world-wide community; and validation, in which other scientists assess the accuracy, quality and importance of the work. Currently, in biology, disclosure and an initial validation are combined in a journal publication. Here, we discuss the advantages of separating these steps into disclosure via a preprint, and validation via a combination of peer review at a journal and additional evaluation by the wider scientific community.

Summary of the ASAPbio Funders’ Workshop

The following is a message from funding agency representatives who attended our recent Funders’ Workshop.

As research funders who attended the ASAPbio Funder’s Workshop for Preprints held at the National Institutes of Health (NIH) on May 23-24, 2016, we wish to provide a brief summary of the meeting. This follows the initial Funder’s Perspective drawn from the first ASAPbio Workshop held on February 16-17, 2016, and continues our desire to be transparent while the community continues to explore the value of preprints to the biomedical research enterprise.

At this workshop, the funders were presented with a summary from the first workshop and the results of a survey conducted by ASAPbio. This was followed by an open discussion of the scholarly and technical goals of a preprint service. The agenda then moved to a discussion of two exemplary models of shared governance of a resource in an international setting, Europe PubMedCentral (Europe PMC) and the Worldwide Protein Data Bank (wwPDB). The final context setting for the funders discussion was provided by representatives of existing and anticipated preprint services,  ArXiv, bioRxiv, PeerJ, F1000 Research, and PLOS. What followed was an open session with all stakeholders present and a closed session involving only the funders.

The consensus of the workshop attendees reflected high enthusiasm about further development of a preprint service for the life sciences. At the end of the day, it was agreed by all in attendance that:

  1.      A preprint policy that is as homogeneous as possible across funders is desired, especially in the way that preprints are considered as part of proposal grant submission and review. A subgroup of funders will draft a concept paper addressing some of the policy issues that might arise when implementing such a preprint policy. This draft will be shared with other funders for their input.
  2.      The funders asked ASAPbio to develop a proposal describing the governance, infrastructure and standards desired for a preprint service that represents the views of the broadest number of stakeholders. The proposal should include a budget, goals, milestones and implementation timeline to bring an appropriate community defined preprint service into operation.
  3.      This letter be distributed as widely as possible to inform all stakeholders of the continued interest by funders in expanding the use of preprints by the life sciences community.

Philip Bourne, The National Institutes of Health
Maryrose Franko, Health Research Alliance
Michele Garfinkel, European Molecular Biology Organization
Judith Glaven, Howard Hughes Medical Institute
Eric Green, The National Institutes of Health
Josh Greenberg, The Alfred P Sloan Foundation
Jennifer Hansen, Bill and Melinda Gates Foundation
Robert Kiley, The Wellcome Trust
Cecy Marden, The Wellcome Trust
Paul Lasko, Canadian Institutes of Health Research
Maria Leptin, European Molecular Biology Organization
Tony Peatfield, Medical Research Council, UK
Brooke Rosenzweig, The Helmsley Trust
Jane Silverthorne, The National Science Foundation
John Spiro, The Simons Foundation
Michael Stebbins, The Arnold Foundation
Nils Stenseth, European Research Council
Carly Strasser, Gordon and Betty Moore Foundation
Neil Thakur, The National Institutes of Health
K. VijayRaghavan, Department of Biotechnology, India

CC-BY-SA Thomas Ulrich, Flickr

Moore Foundation requests grantee feedback on preprint policy

The Data-Driven Discovery group at the Gordon and Betty Moore Foundation released a post on Medium today soliciting feedback on proposed changes to their policies on a variety of open access practices. Preprints are discussed as follows:

Ideally, all journal articles would first be available as preprints. Preprints are versions of your manuscript that are not yet peer reviewed. Many journals allow you to submit articles that have been available as preprints (see this listfor more information). Read more about the benefits of preprints here. Typical places where preprints are deposited for free (read more from Jabberwocky Ecology blog):

  • arXiv (for physics, mathematics, computer science, quantitative biology)
  • bioRxiv (for any biology research)
  • PeerJ Preprints (for biology, medical/health sciences, computer sciences)
  • figshare (for any research)

You can read more and provide input at the post.

Image CC-BY-SA Thomas Ulrich, Flickr

Simons Foundation supports preprints in grants

On May 20, 2016, a Simons Foundation initiative, SFARI, announced that it has changed its policies to support and encourage the use of preprints.

The Simons Foundation Autism Research Initiative (SFARI) recently made two important changes that we hope will help to accelerate the pace of autism research. First, we changed our grant award letter to strongly encourage all SFARI Investigators to post preprints on recognized servers in parallel with (or even before) submission to a peer-reviewed journal. Second, our biosketch form was updated to include space for SFARI grant applicants to list manuscripts deposited in preprint servers; we and our outside peer reviewers will take these manuscripts into consideration when making funding decisions.

Read more on the SFARI website here.

ASAPbio attendees’ commentary in Science

A group of attendees of ASAPbio have published a commentary in the “Policy Forum” section of the journal Science on May 20, 2016. Written by scientists and representatives from journals and funding agencies, the paper serves as a meeting report and summary of opinions on the use of preprints in the life sciences.

Correction: This paper contains a sentence stating that “the median review time at journals has grown from 85 days to >150 days during the past decade.” This is true of Nature, but not journals as a whole. Daniel Himmelstein’s analysis shows that delays across all journals have remained stable.

Photo by N. Cary/Science

Announcing the ASAPbio Funders’ Workshop

On May 24th, 2016, representatives of funding agencies and existing preprint servers as well as junior and senior scientists will meet at the NIH to coordinate their efforts in providing a preprint service for the biology community. The attendees of this small workshop are listed below.

— ASAPbio organizers

ASAPbio Funders’ Workshop attendees

Needhi Bhalla UC Santa Cruz Associate Professor
Philip Bourne NIH Associate Director for Data Sciences
Martin Chalfie Columbia University Professor, Nobel Laureate
Francis Collins NIH Director
Daniel Colón-Ramos Yale University Associate Professor, Organizer
Maryrose Franko Health Reesarch Alliance Executive Director
James Fraser UCSF Assist. Professor, Organizer
Michele Garfinkel EMBO Manager, Science Policy Programme
Paul Ginsparg Cornell University arXiv Founder
Judith Glaven HHMI Senior Science Officer
Eric Green NIH Director, Human Genome Research Institute
Josh Greenberg Sloan Foundation Director DIgital Information Technology
Carol Greider Johns Hopkins Medical School Professor, Nobel Laureate
Jennifer Hansen Bill and Melinda Gates Foundation Officer, Knowledge & Research
Michael Hendricks McGill University Assist. Professor
Jason Hoyt PeerJ PeerJ, CEO
John Inglis Cold Spring Harbor Laboratory bioRxiv Director
Robert Kiley Wellcome Trust Head of DIgital Services, Wellcome Library
Harlan Krumholz Yale University Professor of Medicine
Paul Lasko CIHR Scientific Director, Institute of Genomics
Michael Lauer NIH Deputy Director of Extramural Research
Maria Leptin EMBO Director
David Lipman NIH Director, NCBI
Cecy Marden Wellcome Trust Open Access Project Manager
Elizabeth Marincola PLOS PLOS, CEO
Johanna McEntyre EMBL-EBI Director, Europe PMC
Cameron Neylon Curtin University Former Advocacy Director of the Public Library of Science
Tony Peatfield Medical Research Council, UK Corporate Affairs Director
Jessica Polka Harvard Medical School Postdoctoral Fellow, Organizer
Omar Quintero U. Richmond Assist. Professor
Brooke Rosenzweig Helmsley Trust Program Officer
Jane Silverthorne NSF Deputy Assistant Director
John Spiro Simons Foundation Deputy Scientific Director, SFARI
Michael Stebbins Laura and John Arnold Foundation VP Science and Technology
Nils Stenseth European Research Council U. Oslo and ERC Scientific Council
Carly Strasser Gordon and Betty Moore Foundation Program Officer, Data Driven Discovery Initiative
Neil Thakur NIH Special Assistant to the Deputy Director of Extramural Research
Vitek Tracz F1000Research F1000, Founder
Ron Vale UCSF Professor, Organizer, Lasker Awardee
Harold Varmus Weil Cornell Medical School Professor, Organizer, Nobel Laureate
K VijayRaghavan Dept. of Biotechnology, India Secretary
Richard Wilder Bill and Melinda Gates Foundation Associate General Counsel

An update from ASAPbio

We are writing to inform you about some developments since the first ASAPbio meeting at the HHMI in February. This meeting, which was attended by a diverse group of individuals representing many institutions and followed by a sizable online audience, had an intended goal of learning whether there is increased interest and greater support for the dissemination and use of preprints in the life sciences.  Most, if not all, of the participants arrived at a consensus that preprints could play a wider and more valuable role in the biological sciences.  The atmosphere at the meeting was constructive, several constituencies voiced their ideas about how the wider use of preprints might be achieved, and many ideas about the appropriate next steps were debated.

When the February meeting concluded, several pragmatic issues were left unanswered:

  • Are funding agencies, US and international, interested (perhaps as a consortium) in supporting and sustaining a preprint service for life scientists?
  • Should there be one or multiple preprint servers and, if multiple, how would the information on the servers be coordinated?
  • How should preprint server(s) be governed so that it best reflects the needs of the scientific community?
  • How can information retrieval be made easier for scientists (e.g., by linking preprints, journal publications, and other types of data from the same work)?

Among the encouraging signs at the February meeting was the enthusiasm voiced by several funding organizations for preprints as a means to advance the science they support.  To pursue the funders’ interests expeditiously and in hopes of gathering information that would help answer the above questions, ASAPbio is proposing to hold a smaller and more focused event that will gather representatives of funding agencies (public and private funding organizations from the US and abroad), representatives of several existing preprint servers, data management experts, and prospective users from the life sciences. The NIH has agreed to hold the meeting on their campus, but has not made other commitments to preprint services at this time. The meeting is in an early planning stage; the date, invitation list, and agenda/goals are still being formulated.

To encourage frank discussion and debate about sensitive financial issues at this smaller gathering, we do not expect to use live streaming, as was done at the initial and larger gathering in February. However, ASAPbio will promptly post a detailed summary after the meeting on this web site and encourage participants to publicly discuss their views.  Furthermore, we will continue to use polls and other “feedback” mechanisms via the ASAPbio website to ensure that large numbers of scientists are able to voice their opinions of the type of preprint system they favor.  The first poll is already well underway and we would appreciate your participation; additional polls/feedback are being developed.

In the interim, please feel to contact us with any questions, ideas, or concerns.

Marty Chalfie sends letter to the worm community

GFDL 1.2, by Prolineserver via Wikimedia

GFDL 1.2, by Prolineserver via Wikimedia

Marty Chalfie recently sent the following message to readers of The Worm Breeder’s Gazette:

February 19, 2016

Dear Fellow Worm Workers,

I have just returned from a very exciting meeting on archiving of manuscripts (preprints) in the biological sciences organized by Daniel Colón Ramos, Jessica Polka, Ron Vale, and Harold Varmus (See for more information), and I have become a believer. I am writing to encourage you to join me in changing the way that biological results are made available to the scientific community by submitting your work to an online archive at the same time or even before you submit it for publication in a traditional journal.

Continue reading

Nature article on time to publication

An article by Kendall Powell entitled “Does it take too long to publish research?” appears in the February 11, 2016 issue of Nature. ASAPbio attendees (including Leslie Vosshall and Maria Leptin) and organizer Ron Vale are quoted, and the meeting is mentioned:

This month, a group of more than 70 scientists, funders, journal editors and publishers are meeting at the Howard Hughes Medical Institute campus in Chevy Chase, Maryland, to discuss whether biologists should adopt the preprint model to accelerate publishing. “We need a fundamental rethinking of how we do this,” Vosshall says.