Author Archives: Jessica Polka

Document 5: Existing databases funded by consortiums


Drafted by ASAPbio

arXiv

arXiv is the most directly comparable model in terms of the database content (preprints). Important elements of arXiv’s success are:

  1. single point of ingestion and one-stop shopping for viewing (everyone in the physics community wakes up and searches arXiv),
  2. high visibility and quality (a reason why scientists submit to arXiv to establish priority)
  3. operated for the community good on a not-for-profit basis by a trusted academic institution (Cornell) which has been operating for a century,
  4. funding by a consortium (a major private foundation (the Simons Foundation) and institutions), and
  5. governance by scientists (not just a passive advisory board).

From the arXiv web site:

            In January 2010, Cornell University Library (CUL) undertook a three-year planning effort to establish a long-term sustainable support model for arXiv, one that reduced arXiv’s financial burden and dependence on a single institution and transitioned it to a collaboratively governed, community-supported resource. CUL identified institutions worldwide where the use of arXiv was most active and worked collaboratively with them to develop a membership and governance model based on voluntary institutional contributions. A formal long-term plan took effect in January 2013. In this new model, arXiv is supported by libraries and research laboratories worldwide that represent arXiv’s heaviest users, as well as by CUL and generous matching funds from the Simons Foundation.

Protein Data Bank /Worldwide Protein Data Bank

The protein data bank is a worldwide cooperative of independently supported databases. Thus the wwPDB is a multiple server model based upon geography and geographically located funding agencies.  A common archive of structures is updated and mirrored on all sites, although each site maintains its independence in terms of ingestion and its own web sites (researchers can choose from which site they download).  The incoming data are more complex than those handled by preprint servers, since different types of data are deposited (e.g. X-ray, NMR, etc). Quality control is more of an important issue for structural data than for preprints.  Posting on the PDB is validation (not true for preprints) and constitutes a major part of the PDB mission.  Overall these databases are viewed as being very successful and are reasonably well funded (RCSB alone receives $6.5 million in funding from US government agencies). Arguably, elements of the worldwide collaboration might be subject to inefficiencies and difficulties in governance, but overall the system is also a reasonable model of organizing and distributing information as a public good.

Below Prepared by Stephen K. Burley (Director, RCSB Protein Data Bank)

Protein Data Bank Archive and the Worldwide PDB Protein Data Bank Organization:

The Protein Data Bank (PDB) is the single global archive for experimentally determined, atomic-level structures of biological macromolecules. The PDB archive is managed by the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org) [Berman et al. 2003], which currently includes three founding regional data centers, located in the US (RCSB Protein Data Bank or RCSB PDB; http://rcsb.org), Japan (Protein Data Bank Japan or PDBj; http://pdbj.org), and Europe (Protein Data Bank in Europe or PDBe; http://pdbe.org), plus a global NMR specialist data repository BioMagResBank,

composed of deposition sites in the US (BMRB; http://www.bmrb.wisc.edu) and Japan (PDBj-BMRB; http://bmrbdep.pdbj.org). Together, these wwPDB partners collect, annotate, validate, and disseminate standardized PDB data to the public without any limitations on its use. The wwPDB collaboration is governed by an agreement signed by all four partners (last revised in 2013; http://www.wwpdb.org/about/agreement). The activities of the wwPDB partners are overseen by the wwPDB Advisory Committee, currently chaired by Dr. Andrew Byrd (NCI).

PDB Archive Data Contents:

The PDB archive contains information about structural models that have been derived from three experimental methods, including X-ray/neutron/electron crystallography, NMR spectroscopy, and 3D electron microscopy (3DEM). In addition to the 3D coordinates, the details of the chemistry of the polymers and small molecules are archived, as are metadata describing the experimental conditions, data-processing statistics and structural features such as the secondary and quaternary structure. The structure-factor amplitudes (or intensities) used to determine X-ray structures, and chemical shifts and restraints used in determining NMR structures are also archived. The electron density maps used to derive 3DEM models are archived in EMDB [Lawson et al. 2016] and the experimental data underpinning them can be archived in EMPIAR [Iudin et al. 2016].

wwPDB Partner Responsibilities:

The RCSB PDB provides Data In services for all depositions coming from the Americas (North and South) and Oceania. PDBe provides Data In services for all depositions coming from Europe and Africa. PDBj provides Data In services for all depositions coming from Asia. BMRB archives additional NMR data that are not captured by the other three wwPDB partners during archival data depositions. The RCSB PDB serves as the global Archive Keeper, coordinating weekly updates of the PDB archive with PDBe, PDBj, and BMRB. wwPDB partners distribute identical copies of PDB data from redundant, regional FTP

sites at no charge and with no limitations on utilization. All four wwPDB partners also distribute PDB data at no charge and with no limitations on utilization from their own value added websites in a healthy competition.

wwPDB Partner Funding:

RCSB PDB is supported by NSF [DBI-1338415], NIH, DOE; PDBe by EMBL-EBI, Wellcome Trust [104948], BBSRC [BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1], EU [284209, 675858], and MRC [MR/L007835/1]; PDBj by JST-NBDC, and BMRB by NIGMS [1R01 GM109046].

Governance of the RCSB PDB:

Excerpted from “RCSB Protein Data Bank Advisory Committee Terms of Reference”

The RCSB PDB is managed by two members of the RCSB: Rutgers, The State University of New Jersey and University of California, San Diego, and is funded by the National Science Foundation, the National Institutes of Health, and the Department of Energy through a cooperative agreement. The current Director is Dr. Stephen Burley and the Associate Director is Dr. Helen Berman, who was previously the Director. Both are located at Rutgers. The site head at UCSD is Dr. Peter Rose. In addition, there is a leadership team in charge of key aspects of the RCSB mission including operations, application development, biocuration, data architecture, education and outreach.

The RCSB PDB Protein Data Bank Advisory Committee (RCSB PDBAC) is responsible for providing independent advice to the RCSB PDB Director and staff on current and pending issues of policy, operations, technical implementation, and project performance. The Advisory Committee consists of members chosen from the scientific community, who are recognized experts in their fields, including but not limited to, structural biology, cell and molecular biology, computational biology, information technology, and education. These scientists will be drawn from academia and industry. The AC is appointed by the Director in consultation with other members of the RCSB PDB, the AC Chair, and others. The 3-­year term of membership is renewable.

The RCSB PDBAC meets once a year. The Director is responsible for developing the meeting agenda in consultation with the Chair and, where deemed appropriate, funding agency staff. Meetings typically last a full working day. At the conclusion of each meeting, a written report is prepared by the members of the RCSB PDBAC describing its discussions, including any specific conclusions or recommendations with respect to changes in management and policies of the RCSB PDB. As specified by the cooperative agreement, this report is provided to the Director within 30 days of the AC meeting. The Director formulates a response to the report, addressing recommendations made, issues raised for further consideration, etc., and provides the Chair with the response. The report and the attendant responses are incorporated in the Annual Progress Report submitted to the National Science Foundation.

Europe PMC

The cooperative funding of the European PMC is an interesting model for a consortium.  In this case, each funder supports Europe PMC in proportion to their annual research spend.  One funder (Wellcome Trust) provides the lead role in organizing the consortium. The system of governance involves both the funders and the scientific community.

Prepared by Robert Kiley, the Wellcome Trust

Europe PMC is run, managed and developed by the EMBL-EBI (European Bioinformatics Institute) on behalf of the 26 Europe PMC Funders, which includes the Wellcome Trust, Medical Research Council, Cancer Research UK, the European Research Council and the World Health Organization.

A grant of £5.7M ($8.3M, €7.2M) has been awarded to Dr Jo McEntyre by the Wellcome Trust, on behalf of the Europe PMC Funders.  This grant runs from 2016 to 2021.

Governance

Europe PMC has three governing bodies: the Funders’ Group, Funder Committee and Scientific Advisory Board.

  • The Funders’ Group is made of research funders who both mandate the deposition of research papers which arise from their funding in this repository, and provide funding to facilitate this. It is responsible for setting the overall direction of travel for Europe PMC, and meets annually.
  • The Funder Committee is a subset of the Funders’ Group which meets twice a year to review completed developments, comment on future development and approve the release of funds on behalf of the Funders’ Group.
  • The Scientific Advisory Board meets annually to review progress on the development of the service over the past year, and the plans for development for the forthcoming year. The Board ensures development is sensitive the needs of the scientific community. They also advise the Europe PMC Funder Committee as to the overall effective use of funds from the Europe PMC grant.

Funding

The Wellcome Trust – on behalf of the Europe PMC Funders Group – provides grant funding to EBI to cover the cost of supporting, maintaining and developing the Europe PMC repository.

In turn all the Europe PMC funders (with the exception of the European Research Council, ERC) reimburse the Wellcome Trust according to the payment schedule detailed in the Collaboration Agreement.  ERC’s contribution to funding Europe PMC is made via a grant to the Wellcome Trust.

Each funder supports Europe PMC in proportion to their annual research spend.  This was deemed to be the most equitable way of spreading the costs across all funders.

Additional funders can join the Funders’ Group during the course of the grant by signing an addendum to the Collaboration Agreement.  In turn, EBI can submit development proposals to apply for the additional funds provided by new funders. Such applications are considered by the Funder Committee.

Document 3: Implementation of the Preprint Service


Drafted by ASAPbio

At present, biologists submit very few preprints. However, possible growth to the level of arXiv (100,000 submissions/year) or beyond needs to be considered.  This will challenge the IT capacity (including robust data back-up) and quality control screening systems of existing servers as well as heighten the need to integrate this information.  While still a nascent effort in biology, now is opportune moment to think through a good preprint system that will be accepted by the biology community, have good functionality, and will have lasting value. A particularly important topic for discussion will be whether a consortium of funders will be want to support:

1) a single server for the intake of preprints? or 2) a system for linked, but independent  servers with common standards for quality control and data exchange, etc? Factors to consider for these models:

Maintaining uniform data sharing standards, licensing, and quality control of input. The wwPDB provides an example of a central body that provides standards for multiple PDB servers so that they all contribute in a uniform manner to a single global archive.  This demonstrates feasibility of the multiple server model. However, is it the most efficient model?  If one is to build a system from scratch today, would it be easier to achieve these same goals with one server?

Governance.  A single server supported by the consortium would presumably have one governing body.  With multiple servers, how would governance work for setting standards for integration?  Would funders (or funders/scientists) be involved in the appointments to the advisory boards of individual servers?

International Representation and Involvement.  Preprints are a global resource of knowledge and international involvement is critical for the realization of this vision.  A single preprint server located in the United States with only funding from US agencies may not be perceived as a global resource and attract scientists from around the world. A single server could be supported by a consortium of international funders. Alternatively different preprint servers for different geographic regions could emerge and be supported by regional funding agencies, along the lines of the PDB and PMC.

Overall Cost and Funding Mechanism. Funding of a single server by a consortium of cooperative parties) is relatively straight-forward, but how would that single server be chosen?  Would it be through a competitive call for a contract?  On the other hand, if there are multiple preprint servers, at what level would the funders engage?  Would funders build the IT infrastructure for linking the data?  Or will they be funding the operation of multiple intake servers?  If so, would there be redundant costs for operating several servers versus funding one and would this be mitigated by extra value created?

Long-Term Archival and Preservation.  Preprints should be a permanent record of scientific work and should be backed up. How would the one versus multiple server models affect the implementation of an effective strategy for maintaining a permanent record?

Spurring Innovation. A primary argument for the multiple preprint server model is the potential to promote innovation. arXiv, for example, only has PDF download and no commentary features.  What if a physicist wants a nice HTML web interface for their manuscript and internet commentary on their work? Perhaps multiple, competitive intake servers with different interfaces and features would be beneficial for physicists?   However, with a single server, innovation could be still occur at a level above the initial submission.  With free access to the single server’s API, for-profit or non-profit entities could provide added value, which could include better customized search engines for information, recommendations of work, post-publication peer review, and discussion forums. By separating 1) the initial submission to a highly visible and stable platform (what all scientists want) from 2) additional services (what some scientists want and will be willing to pay for), the market place for innovation can still occur and new ideas tested based upon need and performance. This type of innovation, however, requires that the server be developed with an open API and the right licensing terms.

Do We Know What to Build?  Supporting one server entails risk since it could fail for a variety of reasons. Multiple servers might mitigate risk and perhaps even promote a Darwinian competition with an eventual winner (or with multiple winners each providing value). This market place rationale is reasonable. However, there are also counter arguments and questions.  Will economics (financial support through scientist grants or directly from funders) be sufficient to allow the growth of many flourishing, properly-maintained, and innovative preprint servers?  Can we start by building one consortium-funded server now that will succeed in its goals and not be likely to fail?

An Alternative Model:  Preprints from Journal Submissions

Every journal could develop it own “preprint service” by posting submitted work while in review. One advantage is that the entire process (submission to publication) could be made transparent (an interesting model being pioneered by F1000 Research). Funders would not need to pay for the preprint directly since that cost will absorbed by the journal (but passed along ultimately to the scientist who pays final publication fees). Innovation is promoted since each journal can develop its own preprint style.

Disadvantages are that funders will have to develop a mechanism for creating the preprint database (into PubMed or a new mechanism) from their ingestion through many journals. Furthermore, while some journals accept the majority of submitted manuscripts after peer review, most do not.  This will create a non-viable starting position for many scientists, since a preprint will be linked to a journal that might ultimate reject the work. Furthermore, an important premise of preprints is to circumvent the current problem of judging quality based upon on journal name.

Document 2: A preprint service supported by an international consortium of funders


Drafted by ASAPbio

As a public good, preprints should obey a single data standard that will enable them to reside in a single database.  This database should be permanent, well-maintained, free for all to use, and easily accessible and searchable. This preprint service should have an outstanding governance structure that will represent the needs of the scientific community and oversee adaptations that will be inevitably needed in the future. Further issues regarding the implementation of this preprint service are considered in Document 3.

**As an eventual outcome of this meeting, we recommend the funding of a preprint service in biology by an international consortium of public and private agencies. The contract for this preprint service should support the initial development of infrastructure, yearly operating costs (with the possibility of metric-driven growth), a system of trustworthy governance, and a commitment that the server will not charge submission fees for at least its first five years.** 

The reasons for recommending a single preprint service supported by public/private funding are:

Best chance of adoption by the biology community.  Communication through preprints is foreign to biologists.  Developing a highly-trusted preprint service in the life sciences that is directly supported by major funding agencies and governed by outstanding scientists will promote buy-in to this form of communication.

High visibility.  Scientists want their work to be widely viewed, since this helps them to establish reputation and priority. In the case of arXiv, having a single platform where scientists go to look for new work in the field immensely aids visibility and helps physicist to establish priority of discovery. Maximum visibility also will ultimately require a search engine that integrates preprints with peer-reviewed publication, which should be considered in the initial development of the preprint service as well.

Ensuring trustworthy governance. Direct funding of a preprint service will enable funders to play a more direct role in the governance and future directions of preprints, rather than being relegated to a more peripheral role.  An international component of governance needs to be considered from the onset for this global resource.

Maintaining quality and standards.  A consortium-funded preprint service could help to define quality control for submission and standards for sharing and maintaining data.

Overall cost and ease of funding.  Direct support of a preprint service by a consortium of funders will be small, certainly in comparison to investments made by funders indirectly or directly towards journal publication and the open access of journal publications.  As an alternative to funding a preprint service, funders could provide financial support directly to the scientist to pay for preprint submissions (e.g. as a specific new line item on a grant).  This is similar to the present-day journal system, but in this model, the scientific community and funders have little say in cost and governance.  Furthermore for such a scientist-payer model to take effect globally, all funding agencies would need to develop a new policy allowing scientists to include preprint costs in their budgets.  Even if achieved, this plan is less democratic, as it favors scientists with larger grants versus scientists who have less funds but would like to benefit from preprint use.

Time. There is a sense of momentum and support for the growth of preprints in biology, but this momentum can be lost as quickly as it is being gained. Funders could play a major role in sustaining this momentum by becoming involved and supporting a preprint service. If funders take a lead role, together with the influential junior and senior scientists, then preprints have a chance of becoming common practice in biology.  If funders take a back seat over the next couple of years, if biologist adopt a wait-and-see attitude to see funders become interested, and if preprint submissions tick upward only at a slow rate, biologists will see preprints as a nice idea in theory but a failed experiment in practice.  It might prove difficult to recover from such a situation.

Document 1: Defining Basic Objectives of a Core Preprint Service


Drafted by ASAPbio

Preprints are a global archive of knowledge that serves the public good.

Here, we hope to discuss and define the basic functions that scientists and funding agencies seek from a Core Preprint Service. We use the term “Core” to define the basic features that meet these goals and might define a “minimal viable product”.  Additional services (either for- or not-for-profit) could grow on top of this core.  The needs for good governance and the potential for adaptability are critical, since it may not be possible to build or even envision all elements of an initial core preprint service.

What Scientists Desire:

  • Good visibility of their work. If preprints are difficult to find or behind a paywall, then the purposes of using preprints- to share findings rapidly, to establish priority, and to obtain feedback- are diminished.
  • Credit for their efforts. Preprints need to be acknowledged by funders and universities as component of the evidence of productivity, particularly recent productivity.
  • Easy access to preprints to aid their own research projects. The ability to search the entire preprint archive easily and receive RSS feeds will be appealing to biologists as has proven true for the physicists with arXiv.
  • Easy and no (low) cost author uploads. Like many internet services, being free and easy to use (ie upload) will lower barriers for submission and facilitate wide-spread use in the life science sector.  The option of charging small fees may be possible later, if there is larger scale adoption and possibly added features.
  • The ability to update and submit new versions of the manuscript. Revisions are critical for a preprint service.
  • Freedom to submit to a journal of the author’s choice. Preprints should not be aligned with a single journal or publisher in a way that creates the perception that the preprint server is a preferential ingestion mechanism for specific journals/ publishers.
  • Sustainable model and long-term permanence of submitted work.
  • Governance by well-established and trusted parties. Trust is an important component of a preprint service. Scientists and funders should have a voice in its governance.

Funders desire:

  • Open and rapid communication. The ability to make their supported research openly and rapidly available to the world wide scientific community and thus advance scientific progress.
  • Information to help make funding decisions. The desire to make well-informed decisions on grant applications.  Preprints offer access to the most recent and publicly accessible work from an applicant and facilitate merit-based evaluation of recent productivity
  • Permanence of the scientific record. Stability and permanence of the scientific record (including maintaining different versions of the work).
  • Community support. Excellent leadership and governance from the scientific community, credibility, and wide use.
  • Facility sharing and innovation. The potential for future innovations and change in ways that maximize the funder’s scientific mission, promotes data sharing, and improves scientific evaluation.
  • Upfront quality control to screen for pseudoscientific work and plagiarism. This QC process could include other assurances that fraudulent or low-quality science will not be maintained as a permanent and misleading record.  Preprints will also enable more scientists to evaluate and potentially help to correct work before reaching journal publication.

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.

Some thoughts on ASAPbio


Angela DePace, Assistant Professor, Department of Systems Biology, Harvard Medical School

I believe strongly in open access (mainly because everyone deserves access to the scientific literature, but also because of the immorality of making large profits from free academic labor and the unsustainability of library subscription prices).  I also believe in open peer review; I strive to write critiques that I would be happy to read to the author in person.  It took me longer than it should have to start signing my reviews, but I recently did, and so far so good. I also think that post publication peer review would be a huge step forward for decreasing publication time and increasing the accuracy of the literature, as it would be a more visible record of vetting by the community rather than a select few.

At this stage in my career I’ve come up with a compromise to accommodate these values while still trying to work within the system enough to effectively recruit people and compete for funding, which I think are the things potentially most affected by where I choose to publish.

Continue reading

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

Submission selfies


Take a picture of yourself and/or your coauthors celebrating the submission of a preprint and post it in the comments below (click the icon to at the bottom left of the text field to upload an image). Don’t forget to include a link to the preprint if it’s already available!

You can get a link to each individual comment by clicking “share” underneath it. Please tag with #ASAPbio on social media!

Preprints & Scholarly Publishers: A Synergy


GENETICS and G3: Genes|Genomes|Genetics, peer-reviewed, peer-edited journals published by the Genetics Society of America (GSA), are proud to support the posting of preprints. Here, we outline our experience in a draft statement.

Since 2012, in response to requests from members of our community, the GSA Journals have supported the posting of preprints. In 2015, we were among the first to partner with bioRxiv. Authors can submit a manuscript for peer review at GENETICS or G3 while simultaneously submitting the manuscript to bioRxiv as a preprint. As part of a pilot project, it is now possible to submit preprints from bioRxiv directly to our journals for review. Thus, we and other journals are already conducting the type of experiment proposed by ASAPbio. So far, few authors (<8%) opt to post preprints on bioRxiv before their paper is submitted to our journals for review.

Continue reading

Open pre-print peer review: a call for greater transparency in the evaluation of manuscripts


Lachlan Coin, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
Darya Vanichkina, Centenary Institute, University of Sydney, Sydney, Australia
Alicia Oshlack, Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, Australia

Transparency and openness are extremely beneficial for science.  The immediate and open publication of findings via preprint servers results in rapid dissemination of scientific discovery amongst researchers.   However, under the status quo, preprints are peer-reviewed by journals in a manner which is completely non-transparent to the reader;  and are commonly published in a subscription journal.  As a result, only the draft submission is openly available.  The reviews and the authors’ response are locked away forever.  Readers are asked to trust the journals implicit guarantee that each manuscript has gone through the same robust peer-review process.   However, the reliability of the peer-review process at high profile journals is somewhat of  a myth, as is demonstrated by a trend towards a higher retraction index with higher impact factor [1]. This practice of hiding reviews is damaging to scientific progress and to the general trust in the academic publishing system overall, since readers cannot see which aspects of the study were questioned and whether some aspects – which the reader may consider critical  – were ever questioned at all.

Continue reading

Fix the incentive structure and the preprints will follow


David L. Stern
Janelia Research Campus
HHMI

I have been following the discussion about preprints closely over the past few months and I am won over by the arguments that science papers should be made available freely to everyone as soon as authors feel that the work is complete. Posting papers to preprint servers is one good solution; I imagine there are others. (I prefer to call such documents open papers to remove the stigma associated with calling the work “pre” anything.) However, the discussion about the future of open papers has been imbalanced, with too much emphasis on the consequences of open papers for peer review and too little discussion of the fact that scientists are driven to publish in journals because of the existing incentive structure. The CV, and, specifically, journal names (and impact factors, journal reputation, etc.) are used extensively to judge scientists in competitions for jobs, promotions, and grant money. This is the main impediment to widespread adoption of open papers. I have heard many arguments about how it is too hard to change the structure of these competitions and that we should, instead, focus on producing great science in open papers, and let the culture-shift follow. In contrast, I think it is easier to change the incentive structure first; widespread adoption of open-papers will follow, like water flowing downhill.

Continue reading

Open Scholar: Using Existing Infrastructure to Transform Peer Review


Gary McDowell, Future of Research and Tufts University, and Pandelis Perakakis, Mind, Brain and Behaviour Research Centre, University of Granada, Spain

Please address any correspondence to garymcdow@gmail.com and peraka@ugr.es

In reforming the culture of peer review and moving towards a system that embraces the use and recognition of pre-print servers, we are cognizant of the need to avoid re-inventing the wheel, by identifying and using existing infrastructure and initiatives that can assist in furthering this goal.

Open Scholar (http://www.openscholar.org.uk/, @os_soc) is an open, collectively governed organisation of volunteer researchers that was founded to develop concrete alternatives to the problem of journal-dependent scientific evaluation and communication. We identify the problem of journals and publishers not on whether they offer free or paid access to their content, but on the fact that they all treat knowledge as a material resource that accrues value from exclusivity. However, contrary to material goods, the more knowledge is freely shared, the more value it obtains. It is therefore to the benefit of society and science itself that knowledge, in the form of scientific articles, is made available instantly and in all available means. Such a way to disseminate articles also enforces a private and local way to evaluate them, which brings a lot of perverse incentives in scientists’ collective endeavor. Fortunately, the infrastructure already exists to permit the instant sharing  of all research material. Continue reading

bioRxiv: a progress report


John R. Inglis and Richard Sever, Cold Spring Harbor Laboratory
Please address any correspondence to inglis@cshl.edu and sever@cshl.edu

bioRxiv (biorxiv.org) is a not-for-profit, online archiving and distribution service for preprints[1] of research papers in the life sciences. It was launched in November 2013 by Cold Spring Harbor Laboratory, a research and educational institution, and receives financial support from the Laboratory and The Lourie Foundation.  Scientists have shared their work and ideas through the Laboratory’s meetings, courses, and publications for more than eighty years.  bioRxiv extends that mission for the digital age by enabling scientists to make findings immediately available to the research community worldwide and receive feedback on draft manuscripts before submitting them to journals. There is no charge to post or read papers on bioRxiv. Continue reading

ASAPbio and Preprints – A Perspective from a Junior Faculty Member


James Fraser, UCSF

Can we move towards more open and rapid sharing of scientific results without putting younger scientists careers at risk?  Ideally we want evaluation (of candidates for faculty positions, of promotion of Assistant Professors, of graduate students for fellowships, or of grants for funding) to be thorough and based entirely on a careful study of the science. Young scientists are optimistic about more open and transparent evaluation systems. But we are also worried about the pragmatics of careers as the system is in flux.  Will  preprints be helpful to trainees and junior faculty who are in the most fragile situation with regard to publishing and career advancement?  Could preprints even be harmful to young scientists, perhaps making them vulnerable to getting scooped and thus be dangerous?  My experiences as a non-tenured junior faculty have uncovered many positives of preprints.  My relatively new laboratory (my faculty appointment began in 2013) has started using them and experienced many benefits, and we are not turning back.   Our celebrations when a paper is posted on BioRxiv are joyous and dwarf the, often exhausted, feelings we experience when the work is eventually published in traditional venues. Continue reading