Author Archives: Jessica Polka

ASAPbio newsletter vol 8 – Scientific Society engagement, a new grant, ASAPbio retrospective

Dear subscribers,

Last month, we held a Town Hall meeting for Scientific Societies at NAS in Washington, DC. The meeting featured presentations by representatives of ASAPbio, NIH, and scientific societies who are innovating with preprints and publishing. More information and a video recording of the meeting is available online.

At the meeting, Neil Thakur of NIH shared results of the NIH’s Request For Information (RFI) on the use of preprints & interim research products in NIH grant applications and reports, which were overwhelmingly in favor of preprints. His slides are available to download here.

Also at the meeting, we announced a new $1 million grant to ASAPbio (which recently incorporated as a non-profit) that will help to catalyze the development of the Central Service. For more information about the service, please see our blog post that accompanied the release of an RFA (closing date April 30) and a list of principles and requirements established by funders.

Finally, it’s been a little over one year since our first meeting at HHMI Headquarters in Chevy Chase, MD. While we didn’t realize it at the time, that conference would turn out to be the catalyst for a year of work in promoting a culture of preprinting in biology. To celebrate, we’ve put together an interactive timeline detailing the history of ASAPbio along with major developments in preprint policy. View it here.

Stay tuned for more Central Service developments concerning community governance!

Ron Vale, Founder
Jessica Polka, Executive Director

RFA questions

When questions of general relevance about the requirements and process of the Central Service RFA are received, we will post anonymized summaries of these questions and their answers here. Please direct any additional questions to jessica.polka@asapbio.org.

Bidders’ information meetings

Audio of February 24th, 2017 bidders’ information meeting. The March 29th 9pm EDT meeting had no participants.

Q&A

Q: Can the service include disciplines other than life science?

A: Given the requirement for independent governance, the ASAPbio effort should focus on the life sciences, at least initially. We could explore ways to expand this to other disciplines over time if desirable to other scientific communities. That said, there is nothing to prevent the inclusion of other domains in the service if supported by other funding.

Q: Can the service provide commenting?

A: Section 2B.2C of the RFA reads: “Respondents are also invited to highlight other functionality they would suggest the site should support, although all features and functionality of the CS will require Governance Body approval.” Continue reading

ASAPbio awarded $1 million from Helmsley Charitable Trust for next-generation life sciences preprint infrastructure

Date: Thursday, February 23, 2017
Contact: Jessica Polka | Director, ASAPbio | jessica.polka@asapbio.org

ASAPbio, a biologist-driven project to promote the productive use of preprints in the life sciences, has received a $1 million, 18-month grant from The Leona M. and Harry B. Helmsley Charitable Trust to develop a new service to aggregate life sciences preprints and promote their visibility and innovative reuse

Preprints are complete scientific documents posted online and made freely available to the global scientific community. They are frequently the same version of a paper that is submitted to a journal for peer review. Preprints are widely used in physics, mathematics, and computer science, but are still a new (albeit rapidly-growing) communication system in the life sciences. Mainstream adoption of preprints is challenged by the current difficulties of finding these documents, which are hosted on several unconnected servers; the lack of community governance over the standards that define a preprint; and technological barriers to accessing content for reuse.

The Helmsley award provides funds for ASAPbio to address these problems by constructing a community-governed service that will aggregate, preserve, and deliver life sciences preprints to human and machine readers. It will also develop open-source tools for manuscript screening and conversion to formats such as XML. The guiding principles of this service have been defined by a consortium of funders including the Helmsley Charitable Trust. ASAPbio has issued an RFA to identify potential technical suppliers for the service.

“The grant from the Helmsley Charitable Trust is a giant step forward for the life science community to translate ideas for next-generation preprint services into a reality. This coming summer, we anticipate that other funders will follow the lead of Helmsley and provide further multi-year support for building the technologies for a powerful preprint knowledge repository that facilitates scientific progress through open sharing of data,” says Ron Vale, Founder of ASAPbio. “The support of major funding agencies and the development of new tools for discovering recent scientific findings should encourage life scientists to share their scientific manuscripts in the form of preprints.”

ASAPbio’s work focuses on convening stakeholders for discussions about the role of preprints in the life sciences (namely, an initial conference at HHMI in February of 2016 (see report in Science) and follow-up workshops for funders, technical experts, and scientific societies). Via these meetings, online discussions, and a network of local representatives, ASAPbio seeks to promote the cultural change necessary to complement new developments in technology and policy, from funders, universities, and journals.

ASAPbio is additionally supported by the Alfred P. Sloan Foundation, the Gordon and Betty Moore Foundation, the Laura and John Arnold Foundation, and the Simons Foundation. ASAPbio is incorporated as a nonprofit California corporation.

ASAPbio newsletter vol 7 – Funders sign onto principles for preprint development, RFA released, scientific society town hall

Dear subscribers,

Since the summer of 2016, ASAPbio has been iterating on a proposal for a “Central Service” for life sciences preprints, a database that would aggregate preprints from multiple sources and make them easier to access by humans and machines. We explain the benefits of such a service in a recent blog post.

Yesterday, 11 funders endorsed a set of principles for establishing a Central Service for preprints, and ASAPbio released an RFA to invite potential suppliers to apply to provide it. These developments were covered in articles in Nature, Science, and The Scientist, and more information can be found on the Wellcome Trust, MRC, and NIH websites. We welcome any thoughts or reactions through comments on the web or by email to jessica.polka (at) asapbio.org.

We’re also continuing our engagement with scientific societies. On February 23, we will hold a Scientific Society Preprint Town Hall meeting at NAS in Washington, DC to discuss how preprints can benefit scientific societies in the future. The meeting will feature perspectives from scientists, funders, and societies that are innovating with preprints. Please encourage your scientific societies to attend! More information is available by emailing jessica.polka (at) asapbio.org.

In other exciting news, the list of funding agencies supporting the use of preprints as evidence of productivity is growing: since December, HFSP, Wellcome Trust, MRC, and HHMI have announced new policies on allowing these products to be listed in grants and reports. We’ll continue to monitor these and other developments to policies at funding agencies, journals and institutions.

The Benefits of a “Central Service” for Biology Preprints

Preprints are complete and public manuscripts with associated data shared before undergoing peer review. Physicists, mathematicians, and computer scientists post 100,000 preprints per year to arXiv, a scientist-governed preprint server that has been in operation for over a quarter of a century. Preprints in the life sciences are in a more embryonic stage, with less than 10,000 posted manuscripts per year. However, several meetings hosted by ASAPbio have ended with the conclusion that preprints, in conjunction with journals, hold great potential for enhancing scholarly communication in biology.

Recently, eleven major international funding agencies (Wellcome Trust, National Institutes of Health, Medical Research Council (UK), Helmsley Trust, Howard Hughes Medical Institute (HHMI), European Research Council, Simons Foundation, Canadian Institutes for Health Research, Alfred P. Sloan Foundation, Department of Biotechnology (Government of India), Laura and John Arnold Foundation) have released a statement calling for further technology development and the creation of a central resource for preprints, which is being provisionally called the Central Service (CS). The CS will be a database that aggregates preprints from multiple sources, making them easier to read by humans and machines. These features will enable scientists to find new knowledge that can accelerate their research. The CS will be overseen by a scientist-led governing body, which will ensure its mission in serving the scientific community and the public good.

ASAPbio (a scientist-driven organization to promote the productive use of preprints in biology) has released a Request for Applications (RFA) for the development of this service, which is open to all. After independent reviewers select the preferred applicants(s), and pending commitment of funders, the CS is expected to launch in 2018. Here we discuss why the Central Service is needed and its potential for advancing knowledge dissemination in the life sciences. Continue reading

RFA

ASAPbio is releasing a Request for Applications for the development of a Central Service (provisional name) for preprints in the life sciences issued by ASAPbio. This Request is open to all prospective bidders, and we encourage responses from interested parties able to deliver the services described below. For a concise description of the goals of this project, please see our blog post entitled The Benefits of a “Central Service” for Biology Preprints. Proposals are due on April 30, 2017.

 

 

Principles for establishing a Central Service for Preprints: a statement from a consortium of funders

At the ASAPbio Funders’ Workshop, representatives from a number of funding agencies 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.” Following iterative discussions about the technical and organizational aspects of such a project, ASAPbio is now positioned to issue an RFA for the development of a “Central Service” for preprints. To guide this effort, a group of funders have independently formulated the following principles that will shape the Central Service.

The funders are interested in getting additional funding bodies and research performing organizations to endorse these Principles. If you represent such an agency and are interested in signing on to these principles (or would like to discuss this matter), please contact Robert Kiley, Development Lead, Open Research at the Wellcome Trust (r.kiley@wellcome.ac.uk.)

Continue reading

Societies clarify positions on preprints in grants

Following increased interest in may scientific societies’ positions on the use of preprints in NIH grant applications, several societies have released statements providing their perspectives.

ASCB

The ASCB leadership, after careful consideration, believes preprints should be able to be included in grant applications and referenced in NIH progress reports, with the proper references so they are not confused with peer reviewed published papers. In short, the pace of science is too fast and the process of publication too slow to ignore preprints.

American Society for Microbiology (ASM)

ASM also supports the proposal that NIH allow preprints to be included in grant applications and progress reports, provided they are listed separately from peer-reviewed journal publications, given that they serve different purposes and hold different status.

Genetics Society of America (GSA)

American Society for Biochemistry and Molecular Biology (ASBMB)

While the ASBMB doesn’t oppose preprints being included in grant applications, some members do have concerns about how preprints will be used and whether they will increase the burden on grant reviewers.

ASAPbio newsletter vol 6 – One quick action this week to support preprints

Dear subscribers,

We need your help for an urgent action this week.

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. Several other scientific societies (including Wellcome Trust, MRC, HFSP, Simons Foundation, and the Helmsley Trust) have already implemented new policies on preprint citation in grants in the last 6 months.

FASEB, a scientific society claiming to be the voice of 125,000 scientists, issued a strong negative response to the RFI on 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 of how societies undermined a biology preprint server in 1999, see the open access version of this article).  ASAPbio therefore has written this detailed response to FASEB, which will be sent to FASEB and the NIH.

We are also collecting signatures of scientists who support the option to cite preprints in NIH grant applications and reports until January 23, 2017.  Please take 1 minute to sign your name here if you agree that the NIH should allow the option of citing preprints in grant applications and reports.  These signatures will be sent to the NIH.

Please pass along this message or use your social networks to contact as many of your friends and colleagues as possible.

Thank you for your help!

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