Program

HHMI Headquarters, Chevy Chase , MD
Start: Feb. 16, 5 pm
End: Feb. 17, 6 pm

Program

Accelerating Science and Publication in Biology (ASAPbio)

February 16

5 pm                     Reception, Great Hall, HHMI Headquarters
6 pm                     Dinner, Dining Room
7:00-7:40 pm       Opening Remarks and Meeting Objectives, Auditorium

Advance Material:  “Accelerating Scientific Publication in Biology
Advance Material:  ‘Meeting Objectives’ by Organizers on ASAPbio.org

7:00-7:10                    Ron Vale (UCSF, HHMI)
7:10-7:20                    Daniel Colón-Ramos (Yale University)
7:20-7:30                    Harold Varmus (Weil Cornell Medicine)
7:30-7:40                    Jessica Polka (Harvard Medical School)

7:40-8:10 pm            Keynote Address

Paul Ginsparg (Cornell University),“The Rise of Preprints in Physics, Mathematics and Computer Sciences” (view slides)

8:10-8:20 pm            Questions for Paul
8:20-8:50 pm            Opening comments from participants (<2 min)
9:00-11:00 pm          Social at the HHMI Pub- Pilot Lounge

February 17

7:00-8:00 am              Breakfast, Dining Room

Morning:                   The Policy and Culture of Preprints

(Moderated by Jessica Polka and Ron Vale)

The first session will address three core issues that influence whether scientists decide to use preprints as a form of scientific communication.

8:00-9:00 am             Plenary Talks: (5 min each), Auditorium

Marc Kirschner (Harvard Medical School)
Ruth Lehman (New York University, HHMI)
Martin Chalfie  (Columbia University)
Maria Leptin (EMBL and EMBO)
Elias Zerhouni (Sanofi)
K VijayRaghavan (NCBS and Dept. of Biotechnology, India)
Glenda Gray (South African Research Council)
Randy Schekman (UC Berkeley, HHMI and eLife)
Emilie Marcus (Cell Press)
Harlan Krumholz (Yale University)

9:00-10:30 am           Breakout Sessions  (See Meeting Assignments for rooms; coffee and                                                  refreshments will be available throughout)

Topic 1:   Priority of discovery (recognizing and acknowledging work)

Advance material-   “What defines priority of discovery?” by Ron Vale and Tony Hyman

Why?: The physics community acknowledges a preprint as a means to establish priority of  discovery and to communicate that discovery widely to the community.   Many biologists, in contrast, are uncertain about the role that preprints play in establishing priority.   Some view a preprint as a potential vulnerability, saying that they might get “scooped” by someone who will see their work and rush his or her own competing work into a journal, where it will have greater legitimacy.  This difference highlights the need to establish a community position on how life scientists can fairly communicate their work to the broader scientific community and whether the community will acknowledge the priority of work that has been presented in the form of a preprint and cite it accordingly.  This issue is central to whether or not preprints will become widely used in the life sciences community.

  • Should the posting of a manuscript on a preprint server constitute a legitimate claim to priority of discovery in the life sciences?  What do you think should be the “ground rules” for fairly communicating your scientific work to other scientists? What can we learn from other science communities?
  • Would linking preprints with priority improve our scientific culture and help to clarify who made discoveries? Or would there be undesirable consequences? Discuss specific scenarios based upon your own experiences with competing work.
  • Recognizing that priority of discovery is ultimately defined by the practices of many scientists, how should this topic be communicated and discussed with the larger community?
  1. Using preprints in decision making by funding agencies and promotion committees

Advance material:  “Characteristics of a preprint server”, developed for discussion by Phil Bourne and Daniel Mietchen

Why?  Unlike physics/mathematics, preprints do not play an important role in the current evaluation and reward system for biologists. Many funding agencies, notably the NIH, do not accept preprints as evidence of productivity in grant applications (e.g. as citations in a Biosketch or as work that has come from the past funding period).  Promotion, appointment, and search committees also usually do not know about or consider preprints as part of their decision-making processes.  Might preprints help scientists in their career advancement as well as further the goals the funding agency/promotion committees?

  • Should a paper posted on an acceptable preprint server be used as part of the evidence for evaluating a grant or an appointment or promotion?
  • What value should various kinds of funding agencies place on the use of preprints to communicate information more swiftly? What are the benefits and risks to the funders?
  • Do preprints serve a useful role in the evaluation of grant applications and should it be possible to cite a preprint in a grant application? How should a preprint policy be clarified as part of the instructions to grant applicants?
  • What features could be incorporated into preprint servers to make preprints more useful to funding agencies?
  • Should promotion committees consider preprints in their decision making processes?
  • What criteria for preprint servers should be met for them to be acceptable to major funding agencies? 
  1. Preprints and Journals

Advance material-   “Draft Statement Regarding Pre-posting of Articles”, developed for discussion by The Royal Society, PLOS, eLife, and EMBO Press; and “Sharing Preprints and Publishing Papers, A Symbiosis”, by Bernd Pulverer

Why?  Virtually all physicists and mathematicians who submit their work to a preprint server also ultimately publish the work in a journal.  The ability to post on a preprint server and a journal of their choice also is likely to be desirable to biologists in the near term.  However, not all biology journals will accept work posted as a preprint for consideration for publication or do not have a clear policy.  This creates a confusing situation for scientists, especially given the common scenario of work being rejected by one journal and the need to submit to another.  Can journals and preprints co-exist in biology and can the roles and policies of each be clarified, so that it is easier for scientists to decide how to communicate their work?

  • Should journals acknowledge preprints as a form of scientific communication and publish work that was disseminated previously using this format?
  • Would commentary linked to a preprint on a preprint server help or hinder the traditional, journal-based peer review process?
  • Should there be any general guidelines for authors that would help the coordination of preprint submissions with journal submissions and peer review?
  • How should retraction of specific data or an entire work be handled for preprints?
  • Are there certain types of papers that should not be disseminated without peer review?
  • Are there specific issues concerning preprints that are of such concern to journals that publishers would object to conducing experiments with preprints until the issues have been resolved? What are those issues and what makes them problematic?

10:30-Noon               Reports from the Breakout Groups, Auditorium

10:30-11:00 am         Reports and Discussion- Topic 1

Moderators, Paul Turner (Yale) and Jeremy Berg (U. Pittsburgh)

11:00-11:30 am         Reports and Discussion- Topic 2

Moderators, Chonnettia Jones (Wellcome Trust) and Stefano Bertuzzi                                                (American Society of Microbiology)

11:30- 12:00 am        Reports and Discussion- Topic 3

Moderators, Bernd Pulvere (EMBO Press) and Elizabeth Marincola  (PLOS)

12:00-1:00 pm           Lunch, Dining Room

1:00-1:30 pm             Morning topics: Establishing areas of consensus, next steps of action,                                     and engaging the broader community, Auditorium

Afternoon: Looking Ahead to the Optimal Use of Preprints

(Moderated by Daniel Colón-Ramos and Harold Varmus)

If preprints become more broadly used in the life sciences, they raise interesting possibilities regarding how scientific work is evaluated, how scientists navigate different sources to find information, and how scientific communications are organized on the internet.  These topics will be examined in the afternoon sessions.

1:30-2:30 pm            Plenary Talks (5 min each), Auditorium

Mike Eisen (UCB and HHMI)
Vitek Tracz (F1000)
James Fraser (UCSF)
John Inglis (bioRxiv)
Philip Bourne (NIH)
John Wilbanks (Sage Bionetworks)
Bruce Stillman (Cold Spring Harbor Laboratory)
Johanna McEntyre (PMC Europe)
Robert Kiley (Wellcome Library)
Heather Joseph (SPARC)

2:30-4:00 pm          Breakout Sessions

(See Meeting Assignments for rooms; coffee and refreshments will be available throughout)

Group 1: Evaluating scientific work

Advance material:  “The role of preprints in publishing” by Tracz/Lawrence and “Coupling Pre-Prints and Post-Publication Peer Review for Fast, Cheap, Fair, and Effective Science Publishing” by Eisen/Vosshall

Why?   Currently, scientific work is evaluated through anonymous peer review initiated through a journal. The visibility of the scientific work is also highly influenced by the specific journal in which the work appears.  But the best and most interesting work may not always surface to the top through this system.

  • What new ideas and experiments in peer review, scientific exchange, and evaluation of scientists might be facilitated by preprints?   Can one think of a “preprint” as the publication followed by a second phase of an open post-publication reviewing process that leads to community evaluation and status? How might those experiments be tested and evaluated?
  • Will open reviewing of work (e.g. through a comment system on a preprint) improve or complicate evaluation? Should comments even be added to preprints (available on bioRxiv but not arXiv)? Should commenting be done anonymously or non-anonymously? How might those experiments be tested and evaluated?

Group 2:  Finding the information that scientists need

Why?: Finding and synthesizing information is critical for one’s success as a scientist.  It is thus relevant to consider what types of information might be linked to preprints to facilitate interpretation of the data. Given that we live in an age of information overload, how might the additional information created by preprint servers be managed so that scientists can sift through preprints and find relevant information.

  • What improvements can be made to preprints (e.g. associated large data sets, videos, novel ways to organize the presentation of findings, etc)?
  • What kinds of tools and evaluation methods can and should be used to help readers search for material by topic, date, and investigator as well as stratify preprints by quality, viewership, significance, novelty, etc? 

Group 3:  Organizing scientific work on the internet

Why?: Preprints and journals will reveal different versions and stages of the same scientific work, raising questions of how they should be linked to one another, how they should be cited, and even whether new terminology should be applied (since “print” is not part of the current medium).  Also, most scientists now use PubMed, which does not house preprints.  Scientists will want to search for research papers both on preprint servers and journals in a time-efficient manner.

  • What is the best system for housing life science manuscripts on the internet once they have been posted without peer review?  Should any criteria be applied for governance and perpetuity of display of manuscripts? (related to discussion in morning group 2).
  • How should preprints be made discoverable? Should they be incorporated as a new component of PubMed (and PubMed Central) or should they be maintained in a separate place?
  • What should be done to preserve different versions of a manuscript and their chronological relationship? Should any informal comments or formal reviews also be linked to the different versions?
  • Do we need new terminology to describe the various stages of a scientific report?

4:00-5:00 pm             Reports from the Breakout Groups, Auditorium

Moderators Group 1: Judith Glaven (HHMI) & Leslie Vosshall (Rockefeller, HHMI)

Moderators Group 2: Jennifer Lippincott-Schwartz (HHMI, NIH) & Thierry Galli (INSERM)

Moderators Group 3:  Cynthia Wolberger (Johns Hopkins University) & Yochai Benkler (Harvard Law School)

5:00-6:00 pm             Afternoon topics: Establishing areas of consensus, next steps of action,                                  and engaging the broader community, Auditorium

6:00 pm                      Departure, for those leaving

Dinner in the Dining Room for those staying

7:00-9:30 pm             Social, Pilot Lounge

February 18

7:30-8:30 am             Breakfast (Dining Room) and Departures