Category Archives: News

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

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.

As many of you know manuscripts in physics, mathematics, computer science, nonlinear sciences, quantitative biology and statistics are almost universally submitted to ArXiv.org, so they are available to interested readers when the authors feel they should be made public. Approximately 80% of these manuscripts are also submitted to traditional journals, sometimes with modifications suggested by readers and even new coauthors. Submission to arXiv has become the standard in these fields. Similar archives have been developed for the biological sciences (See http://asapbio.org/resources). Most journals already permit preprint archiving (the biggest exceptions are the Cell Press journals; See https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy and http://www.sherpa.ac.uk/romeo/journalbrowse.php?la=en&fIDnum=|&mode=simple).

From the discussions at ASAPbio, I have come away with the following thoughts. First, manuscript submission to an open archive will speed up science. The current system of manuscript submission to journals [with review, editorial evaluation at various stages (and all to often resubmission and review), and embargo] means that work ready for public distribution is delayed for months and even years. Depositing the manuscript in a preprint archive will eliminate this downtime (even more so when the manuscript may have to be submitted to another journal). Moreover, a broader audience will have time to help improve the manuscript before its final publication. Second, the work will be universally available. All scientists and interested readers, especially those not associated with rich institutions or countries, will have equal access to the material. As such, manuscript archiving is an important step in democratizing scientific information. Third, submission to a manuscript archive establishes a time stamp documenting when results and ideas were first presented to the general scientific community. Not only can such a time stamp demonstrate priority, but because multiple version of the work can be archived, this repository can help future science historians follow the development of ideas and discoveries. Fourth, the general consensus at the meeting was that such manuscripts, even though not peer reviewed, should be considered for hiring, promotion, and grant reviews (although we all have to work on our institutions to enable this change). Such a change not only allows a more inclusive view of a person’s work, but frees these review decisions from the vagaries of the manuscript reviewing process.

What am I going to do? When I returned to the lab, I found an email asking for a revision of a paper we had previously submitted to Mol. Biol. Cell. Today, we submitted our revised manuscript both to the journal and to bioRxiv.org. We will submit our future manuscripts and revisions simultaneously to bioRxiv.org and the journals we wish to publish in. We welcome comments, suggestions, and criticisms of this work as it goes online and hope that the more rapid dissemination of our results will be helpful to others.

What can you do? The C. elegans community has always been known for its collegiality and helpfulness. The Worm Breeders Gazette was established so researchers could share their work with the community and for many years it served to promote collaboration, excitement, and camaraderie. I hope that submission of all our work to bioRxiv.org or another archive will continue this tradition and help all of our research.

All the best,

Marty Chalfie

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

Share your ideas on accelerating scientific publishing

Most scientists agree that the research in biology could be accelerated and improved if scientific publishing was made easier, faster, and more transparent. On February 16th and 17th, ~70 members of the science community, young and old, leaders and trainees, and representatives of journals, scientific societies, academic institutions, and funding agencies, will convene at the Howard Hughes Medical Institute in Chevy Chase, Maryland to discuss ways in which “preprints” might facilitate this goal.

Preprints allow scientific findings to be posted immediately, without peer review, in a format freely accessible to anyone in the world. They can help scientists receive productive feedback on their work and also could serve as evidence for productivity. While preprints have been a key component of knowledge sharing within the physics community for decades, they are not widely used in biology because they are incompatible with the policies of some journals, not officially acknowledged by many funding agencies, and not clarified with regard to their role in establishing priority of discovery in the biology community. The ASAPbio meeting specifically focuses on how preprints can be used optimally and fairly to: 1) advance progress in the life sciences, and 2) meet the needs of scientists at all stages of their careers and world-wide.

We recognize that the ASAPbio meeting will be composed of a mere ~70 individuals, yet the success of the meeting will be determined ultimately by the opinions and actions of many scientists, representatives of funding agencies, publishers, and others who are not physically present.  For that reason, we will stream the meeting online so that all can watch and foster participation.

You are invited to visit ASAPbio.org to take a 3-minute survey to share your opinions on preprints, comment on white papers written by attendees, and register your opinions via Twitter with #ASAPbio. Tune in at ASAPbio.org at 7 pm Eastern Time on Tuesday, February 16th, to watch the opening of the meeting, including a keynote address by Paul Ginsparg, the founder of the physics preprint server arXiv. You can also view a stream of all plenary talks and discussion on February 17th starting at 8 am. Throughout the whole meeting, viewers are encouraged to submit comments and questions on Twitter with the hashtag #ASAPbio.