For reproducibility, we need the methods behind the data

2018/19 eLife Ambassadors progra

In broad daylight: Innovation and transparency in peer review

Independent peer review is one of the foundations of scholarship and a practice that has been in place in the academy for centuries. This panel will address innovations that promote transparency and accelerate the pace of research, such as post-publication review, open peer review, and research evaluation ethics, exploring questions such as: • Who qualifies as a peer reviewer? • What kinds of content should be reviewed? Datasets? Editorials? • What are the strengths and weaknesses of pre-publication vs. post-publication peer review? • Is open peer review integrated with the formal publication process? Does it need to be? • What concerns are there with making peer review open? Are there benefits to anonymity, for example? • How do we ensure productive and civil discourse in a public review process? • How do these innovations change the relationship between the reviewer and the author? • Is it important to address the novelty and significance of the research in the review, or should it be only about content and soundness? • What is the anticipated trajectory of these changes in peer review and how might they affect research 25 years from now? This presentation was given during Open Access Week 2015, jointly sponsored by the Carnegie Mellon University Libraries and the University Library System, University of Pittsburgh on Monday, October 19, from 4:30 - 6:00pm at the University Club, University of Pittsburgh. The panel discussion was preceded by a poster session featuring research support services offered by the University Library System. ABOUT THE PANELISTS: Jackie Smith (Moderator) is Professor of Sociology and editor, Journal of World-Systems Research. Larry Kane is Associate Professor in the Dept. of Immunology at the University of Pittsburgh. As a member of the Faculty of 1000, Dr. Kane is avid contributor to F1000Prime and F1000Research, and is an advocate for innovation in the peer review process to accelerate the dissemination of research. F1000Research (f1000research.com) is an Open Science publishing platform offering immediate publication of posters, slides and articles with no editorial bias. All articles benefit from transparent peer review and the inclusion of all source data. Josh Nicholson is the founder of The Winnower, an open scholarly publishing platform launched in 2014. The Winnower acts as a publisher and archiver for a variety of content (research,reddit AMAs, student essays, journal club proceedings, peer reviews, open letters, grants, etc.) and to-date has published over 600 articles. Nicholson received his PhD in cell biology in 2015 from Virginia Tech. He has authored numerous articles on scientific funding and publishing in addition to his research on cancer, some of which have been discussed in The Economist, The Boston Globe and other major news outlets. Brandon Stell is a neuroscientist and team leader at the French national science organization CNRS in Paris and is the President of the PubPeer Foundation. PubPeer (pubpeer.com) is an anonymous online forum for post-publication peer review where scholars can comment on any article published with a DOI. The authors of the paper are invited to engage with the commenters. Lenny Teytelman is a geneticist and computational biologist. Since 2012, he has devoted himself to creating protocols.io: a free and up-to-date central repository of life science methods. As cofounder of protocols.io Lenny brings a strong passion for sharing science and improving research efficiency through technology

Protocols.io: For reproducibility, we need the methods behind the data

"Protocols.io: For reproducibility, we need the methods behind the data" was presented at the ORCID Northern California Workshop at UC Berkeley on May 15, 2018 by Lenny Teytelman (Protocols.io).<p></p

Getting Started with protocols.io

Harvard Medical School 2-hour workshop on "Getting Started with protocols.io

When publishers aren’t getting it done

A panel discussion at AAUP on scholar-led publishing projects

VERVENet: the viral ecology research and virtual exchange network

ABSTRACT 33 The advent of metagenomic methods to sequence DNA directly from an environment has revolutionized 34 viral ecology, making it possible to &quot;see&quot; natural viral communities that could not be previously studied This need is even more apparent in emerging fields such as aquatic viral ecology where lab, field, and 58 bioinformatics methods are being actively developed in a subset of labs given the experimental nature of these methods, the virus ecology community has expressed a need for 60 fostering discussions about these protocols towards improved methodologies and to increase connectivity 61 and collaboration among researchers. The challenge is to develop a method-centered collaborative 62 platform that recapitulates the functionality of a scientific meeting -a digital community for connecting 63 with fellow researchers to share and discover the state of the art. 64 65 Here, we present the Viral Ecology Research and Virtual Exchange Network (VERVENet), a 66 collaboration between the University of Arizona and protocols.io, to deliver an online forum for the virus 67 ecology community. This forum promotes scientific communication and collaboration to (i) fuel 68 connectivity among viral ecology researchers for sharing data sets, knowledge, job postings, conference 69 announcements through a common online forum called VERVENet, (ii) share protocols and their 70 annotations and optimizations, and (iii) facilitate literature discovery through personalized 71 recommendations to promote discussion on cutting edge viral ecology research. Through interconnecting 72 these valuable resources, we have developed a &quot;go-to&quot; site for viral ecology research (2016k). Moreover, 73 these tools are broadly useful to any community or individual lab for promoting scientific inquiry, 74 PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.1901v1 | CC-BY 4.0 Open Access

Reproducibility for everyone: a community-led initiative with global reach in reproducible research training

Reproducibility is a cornerstone of the scientific method and sets apart science from pseudoscience. Unfortunately, a majority of scientists have experienced difficulties in reproducing their own or someone else’s results. This inability to confirm scientific findings negatively impacts individual scientists, funding bodies, academic journals, pharmaceutical drug development and the public’s perception of science. Factors causing irreproducible results can arise from nearly every aspect of the scientific process, and typically reflect a lack of in-depth training in reproducible research practices. Here, we present the Reproducibility for Everyone (R4E) initiative, a collaboration between researchers from diverse scientific disciplines and industry partners who aspire to promote open and reproducible research practices. We have developed a customizable workshop series targeting researchers at all levels and across disciplines. Our workshop series covers the conceptual framework of reproducible research practices followed by an overview of actionable research practices. To date, we have reached more than 2000 researchers through over 25 workshops held at international conferences and local meetings. By incorporating further contributions from the scientific community, we hope to expand this valuable resource for teaching transparent and reproducible research practices. Our initiative demonstrates how a shared set of materials may form the basis for a global initiative to improve reproducibility in science. The workshop materials, including accompanying resources, are available under a CC-BY 4.0 license at www.repro4everyone.org

Science Forum: A community-led initiative for training in reproducible research

Open and reproducible research practices increase the reusability and impact of scientific research. The reproducibility of research results is influenced by many factors, most of which can be addressed by improved education and training. Here we describe how workshops developed by the Reproducibility for Everyone (R4E) initiative can be customized to provide researchers at all career stages and across most disciplines with education and training in reproducible research practices. The R4E initiative, which is led by volunteers, has reached more than 3000 researchers worldwide to date, and all workshop materials, including accompanying resources, are available under a CC-BY 4.0 license at https://www.repro4everyone.org/

Science forum:A community-led initiative for training in reproducible research

Open and reproducible research practices increase the reusability and impact of scientific research. The reproducibility of research results is influenced by many factors, most of which can be addressed by improved education and training. Here we describe how workshops developed by the Reproducibility for Everyone (R4E) initiative can be customized to provide researchers at all career stages and across most disciplines with education and training in reproducible research practices. The R4E initiative, which is led by volunteers, has reached more than 3000 researchers worldwide to date, and all workshop materials, including accompanying resources, are available under a CC-BY 4.0 license at https://www.repro4everyone.org/

Open Letter to The American Association for the Advancement of Science

This is an open letter concerning the recent launch of the new open access journal, Science Advances. In addition to the welcome diversification in journal choices for authors looking for open access venues, there are many positive aspects of Science Advances: its broad STEM scope, its interest in cross-disciplinary research, and the offering of fee waivers. While we welcome the commitment of the Association to open access, we are also deeply concerned with the specific approach. Herein, we outline a number of suggestions that are in line with both the current direction that scholarly publishing is taking and the needs expressed by the open access community, which this journal aims to serve