Category Archives: News

ASAPbio response to FASEB’s statement on the NIH RFI on preprints


1/19/2017 update: We will close the signature drive at 9pm EST on Sunday, 1/22/2017.

Summary

The NIH released a RFI (request for information) on “including preprints and interim research products in the NIH applications and reports.”  ASAPbio, and many individual scientists, responded with arguments in favor of providing scientists with the option, not requirement, of citing preprints in NIH applications/reports as public evidence of their most recent work and productivity. FASEB, a scientific society claiming to be the voice of 125,000 scientists, issued a strong negative response to allowing preprints to be used in NIH grant review.  We, junior and senior scientists of the ASAPbio Board of Directors feel that there are many deeply problematic issues with FASEB’s arguments including 1) an unfamiliarity with preprints and even an articulation of incorrect information, 2) a lack of transparency of how they derived their decision, and 3) a view that there is “no need to read” original scientific papers, which we feel is not the type of culture that the funding agencies should foster in order to promote excellence in grant review. Because FASEB claims to speak for many societies and many scientists, their letter (signed only by the FASEB President) could be given disproportionate weight by the NIH (for a past historical example, see this article).  ASAPbio therefore has written this detailed response to FASEB (see below). We are also collecting signatures of scientists who support the option to cite preprints in NIH grant applications and reports here until 9pm EST on 1/22/2017.

Continue reading

Update on development of a Central Service Request for Applications (RFA)


At the ASAPbio Funders’ Workshop in May of 2016, representatives of funding agencies requested that ASAPbio “develop a proposal describing the governance, infrastructure and standards desired for a preprint service that represents the views of the broadest number of stakeholders.” Toward this end, we proposed a model for a “Central Service” (CS) that would aggregate content from multiple preprint servers, facilitating human and machine access to preprints via a search tool and an API.

Three separate processes are now ongoing to define this service:

Continue reading

ASAPbio newsletter vol 5 – Tell the NIH what you think about preprints, Crossref service launches today, new resources


Dear ASAPbio subscriber,

Tell the NIH what you think about preprints

The NIH has recently released a request for information (RFI) on the use of preprints and other interim research products. We encourage all interested parties to respond to the RFI using the submission website by the deadline of December 9th (extended from November 29th).

ASAPbio’s draft response is posted here. Even if you completely agree with our draft, we encourage you to submit your own responses as well. A large number of responses will be critical in conveying a strong message of community interest in preprints and other interim research products to the NIH. Responses from individual scientists at all career stages are encouraged. You do not have to respond to all questions, and the responses can be short. If you would like to share comments or your own response to the RFI, please use the comment section below the post.

Crossref launches preprint service

Today, Crossref, the organization that assigns DOIs for journal articles, launches their preprint service! The service will offer a specialized content type for preprints, enabling them to be linked to their corresponding journal article. This development will make it easier for preprint servers and journals to display links (backwards and forwards) between different versions of the same article, and it will facilitate pooling of metrics, citations, etc between the versions. This is a landmark in the development of preprints as an integral part of the scholarly literature.

New resources at ASAPbio.org

How many life sciences preprints were posted in September 2016? Which journal now has Preprint Editors? Which funder is requiring preprint deposition? And which med school accepts preprints in tenure packages?

We’re now tracking the growth of preprints in the life sciences as well as new developments in funder, university, and journal practices and policies regarding preprints. You also can now view all of these newsletter posts (including this one) on the web. Finally, we printed stickers (below) to help create visibility and spark conversations about preprints. Just fill in the form at asapbio.org/stickers to request some!  

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Best,
Jessica Polka
Director, ASAPbio

ASAPbio’s response to the NIH RFI on preprints


Note: the RFI is now closed. The NIH has announced a policy that encourages the use of preprints.

The NIH has recently released a request for information (RFI) on the use of preprints and other interim research products. We encourage all interested parties to respond to the RFI using the submission website by the deadline of December 9th 2016 (extended from November 29th).

ASAPbio’s draft response is posted below. Even if you completely agree with our draft, we encourage you to submit your own responses as well. A large number of responses will be critical in conveying a strong message of community interest in preprints and other interim research products to the NIH. Responses from individual scientists at all career stages are encouraged. You do not have to respond to all questions, and the responses can be short. If you would like to share comments or your own response to the RFI, please use the comment section below the post.
Continue reading

ASAPbio newsletter vol 4 – Technical workshop, new website features, ambassadors


Dear ASAPbio subscriber,

Here’s what’s new:

  • We held a successful Technical Workshop to discuss the feasibility of creating a central preprint service. All the notes are online, and you can also view the archived video stream.
    • We’re working on a request for information to identify potential suppliers, their implementation strategies, and their predicted costs and development timescales. We will present all reasonable responses to a group of funders as part of our response to a request that emerged from the ASAPbio Funders’ Workshop. More details about our planned process can be found here.
  • We’ve added some new features to the website.
  • The ambassador program kicked off in earnest.
    • Check out the map to see who’s near you.
    • It’s also not too late to sign up – we’re looking for people willing to act as local points of contact about preprints. We’re also providing resources to help ambassadors give talks about preprints at their home institutions or while traveling to conferences and other meetings.

Please let us know if you hear of any exciting developments in preprints in life sciences!

Jessica

Jessica Polka, PhD

Director, ASAPbio

ASAPbio newsletter vol 3 – REQUESTING FEEDBACK on a central preprint service for biology


Dear ASAPbio subscriber,

It’s been an exciting few months at ASAPbio! Here’s what’s happened:

  • The report of our February meeting at HHMI was published in Science, and Ron Vale and Tony Hyman recently published an article about priority of discovery & preprints in eLife.
  • ASAPbio was awarded grants totalling $400,000 in provisional funding from the Arnold, Sloan, Simons, and Moore foundations for a period of 18 months.
  • We held a Funders’ Workshop at the NIH on May 24th.
  • As an output of this, representatives from funding agencies called for ASAPbio to develop a proposal for a preprint service for biology.
  • In response to this request, we’re now seeking feedback from the community on a draft proposal for a central preprint service that could aggregate content from multiple servers. Please consider leaving a public comment on the web and sharing the link with your networks. After future iterations, we will present several variations to funders in the fall.
  • To develop the technical aspects of this proposal, we’re hosting a Technical Workshop in Cambridge, MA on 8/30. We’re aiming to provide a video stream so that anyone can follow along.

Finally, effective 8/1, I’m now serving as full-time director of ASAPbio! Please don’t hesitate to contact me with any comments, questions, or ideas on how we can work together to advance the productive use of preprints in biology.

Best,

Jessica Polka, PhD

Director, ASAPbio

Four foundations announce support for ASAPbio


This announcement was originally posted on the Simons Foundation website.

On June 20, four foundations announced their support for ASAPbio (Accelerating Science and Publication in Biology), a scientist-driven effort with a mission to promote the use of preprints in the life sciences. The combined total provisional funding — from the Alfred P. Sloan Foundation, the Gordon and Betty Moore Foundation, the Laura and John Arnold Foundation and the Simons Foundation — is $400,000 for work to be conducted over the next 18 months.

The hope is that use of preprints will catalyze scientific discovery, facilitate career advancement and improve the culture of communication within the biology community. Continue reading

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

ASAPbio newsletter vol 2 – Your help requested for the ASAPbio Funders’ Workshop


Dear ASAPbio subscriber,

Last week, we announced the ASAPbio Funders’ Workshop, a small meeting to be held at NIH on May 24th to coordinate support among private and public funding agencies for preprints in biology. Representatives from existing preprint servers will attend, as will some junior and senior scientists.

To ensure that the voice of the community is well-represented at the workshop, we need as many responses as possible to our new, updated survey on preprint server preferences by May 20th.

Please consider sharing the following announcement with your lab, department, society, social media network, or other interested group:

Help shape the future of preprints with ASAPbio’s 10 minute survey

On May 24th, representatives of major funding agencies and existing preprint servers will convene at the NIH for the ASAPbio Funders’ Workshop. The goal of this meeting is to coordinate efforts to support a preprint service with maximum benefit for the biology community. In order to make informed decisions, the attendees of this meeting need to hear from practicing scientists like you. Please take 10 minutes to complete our updated and expanded survey at ASAPbio.org by May 20th! We’ll raffle off 50 ASAPbio t-shirts to survey participants, but more importantly, the opinions of all respondents will help shape the future of how we communicate results in biology. Please share the survey with your colleagues via email and social media using #ASAPbio.

Best,

ASAPbio organizers

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.

ASAPbio newsletter – vol 1


Thanks for subscribing to ASAPbio’s newsletter!

As part of the followup to last month’s productive meeting, ASAPbio organizers and attendees have been working to spread discussions about preprints to the broader community. Recent articles at Wired, NYTimes, and The Economist have certainly moved the needle in this regard!

Please help keep the conversation going by taking one or more of the following actions:

  1. Take the survey on preprint preferences here. We’re trying to understand what attributes of preprint servers are most desired by the community – and whether one or several would be most beneficial. You responses will remain confidential.
  2. Post a submission selfie – take a photo of yourself and your coauthors celebrating a preprint submission and post it here.
  3. Become an ASAPbio AmbassadorSign up to act as a representative for ASAPbio efforts at your institution. We’ll get in touch to provide materials to make organizing local “town hall” events easier. We are preparing this material now and it should be available within one month at the preprint info center on ASAPbio.org.
  4. Help us keep track of progress by leaving a comment with any news (a change in journal policies, a local event – even in the early stages of organization – a new article, etc,)  here.

Best,

ASAPbio organizers

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 asapbio.org 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.

Wellcome Trust: draft statement on data sharing in public health emergencies


Following discussions with several funder and journal colleagues, we believe that it would be extremely powerful and timely to publish a short joint statement emphasising our commitment to ensure that results and data relevant to the current Zika crisis and future public health emergencies should be made as available as rapidly and openly as possible.

The text of our statement follows below. Given the time critical nature of this, and deadlines for several of our journal colleagues, we propose to finalise and publish this statement by 22:00 GMT (17:00 EST) tomorrow – Wednesday.

We would like as many funders and journals to join us possible. I would be very grateful if you could let Katherine Littler (K.Littler@wellcome.ac.uk) know by 15:00 GMT on Wednesday if your organisation would be willing to sign.

Draft statement

The case for sharing data, and the consequences of not doing so, have been bought into stark relief by the Ebola and Zika outbreaks.

In the context of a public health emergency of international concern, there is an imperative on all parties to make any information available that might have value in combatting the crisis.

As research funders and journals, we are committed to working in partnership to ensure that the global response to public health emergencies is informed by the best available research evidence and data, as such:

  • journal signatories will make all content concerning the Zika virus free to access. Any data or preprint deposited for unrestricted dissemination ahead of submission of any paper will not pre-empt its publication in these journals.
  • funder signatories will require researchers undertaking work relevant to public health emergencies to set in place mechanisms to share quality-assured interim and final data as rapidly and widely as possible, including with public health and research communities and the World Health Organisation.

We urge other journals and research funders to make the same commitments.

This commitment is in line with the consensus statement agreed at a WHO expert consultation on data sharing last year whereby researchers are expected to share data at the earliest opportunity, once they are adequately controlled for release and subject to any safeguards required to protect research participants and patients.

Very best wishes,

Jeremy

Dr Jeremy Farrar
Director, Wellcome Trust