eLife is pleased to announce Fiona Hutton as its new Head of Publishing.
Originally a life scientist specialising in cancer virology, Hutton brings 20 years of STM publishing experience to eLife, including her most recent positions as Head of STM Open Access Publishing and Executive Publisher at Cambridge University Press, UK. She formally begins her role with eLife today, taking over from Interim Head of Publishing Peter Rodgers.
“DOIs or Digital Object Identifers have become ubiquitous in our Scholarly ecosystem to the point that I find most researchers today are at least vaguely familar with the idea. You can possibly blame Sci-hub for this, but today many other tools and systems are comfortable with asking for DOIs without feeling the need to explictly explain what they are.
Similarly librarians even those not in the Scholarly Communication know of DOIs. Most of us know DOIs are meant as a unique persistant identifer for articles but having a DOI has no bearing on the quality of the article.
Still knowing of DOIs is not the same of actually having good or detailed understanding….
But a new paper in the journal PLoS Biology argues that, while the swell of the open science movement is on the whole a good thing, it isn’t without risks.
Though the speed of open-access publishing means important research gets out more quickly, it also means the checks required to ensure that risky science isn’t being tossed online are less meticulous. In particular, the field of synthetic biology—which involves the engineering of new organisms or the reengineering of existing organisms to have new abilities—faces what is called a dual-use dilemma: that while quickly released research may be used for the good of society, it could also be co-opted by bad actors to conduct biowarfare or bioterrorism. It also could increase the potential for an accidental release of a dangerous pathogen if, for example, someone inexperienced were able to easily get their hands on a how-to guide for designing a virus. “There is a risk that bad things are going to be shared,” says James Smith, a coauthor on the paper and a researcher at the University of Oxford. “And there’s not really processes in place at the moment to address it.”
Over the last month, we have added two new groups, GigaScience and GigaByte, from the journals of the same name, increasing the number of specialist teams displaying their evaluations on Sciety.
GigaScience and GigaByte are part of GigaScience Press. With a decade-long history of open-science publishing, they aim to revolutionise publishing by promoting reproducibility of analyses and data dissemination, organisation, understanding, and use. As open-access and open-data journals, they publish all research objects (publishing data, software and workflows) from ‘big data’ studies across the life and biomedical sciences. These resources are managed using the FAIR Principles for scientific data management and stewardship, which state that research data should be Findable, Accessible, Interoperable and Reusable. They also follow the practices of transparency and openness in science publishing, and as such, they embrace open peer review (which is mandated for both journals) and preprints (which are strongly encouraged in GigaScience and mandated for GigaByte). The opportunities for combining both are covered by GigaScience in its video on open science and preprint peer review for Peer Review Week.
“All three journals will publish under an Open Access model and embrace Open Science policies to help support the changing needs of academics in these fast-moving research areas. There will be direct links to preprint servers and data repositories, allowing full reproducibility and rapid dissemination of published papers to help accelerate the pace of research. Each journal has renowned Editors in Chief who will work alongside a global Editorial Board, delivering robust single-blind peer review. Supported by our internal editorial teams, this will ensure our authors will receive a quick, user-friendly, and personalised publishing experience….”
Abstract: The ideal of self-correction in science is not well served by the current culture and system surrounding amendments to published literature. Here we report on a survey (N = 132) that highlights academics’ dissatisfaction with the status quo and their support for an alternative approach. We then describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. Here authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository or similar) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and, as such, requires nothing but buy-in from the scientific community – a community that is already evolving towards various open science frameworks. This would remove a number of frictions that discourage amendments thus leading to an improved scientific literature and a healthier academic climate.
Abstract: To respond to the NIH’s policy for rigor and reproducibility in preclinical research, many journals have implemented guidelines and checklists to guide authors in improving the rigor and reproducibility of their research. Transparency in developing detailed prospective experimental designs and providing raw data are essential premises of rigor and reproducibility. Standard peer reviews and journal-specific technical and statistical reviews are critical factors for enhancing rigor and reproducibility. This brief review also shares some experience from Arteriosclerosis, Thrombosis, and Vascular Biology, an American Heart Association journal, that has implemented several mechanisms to enhance rigor and reproducibility for preclinical research….
Double-blind conferences have engaged in debates over whether to allow authors to post their papers online on arXiv or elsewhere during the review process. Independently, some authors of research papers face the dilemma of whether to put their papers on arXiv due to its pros and cons. We conduct a study to substantiate this debate and dilemma via quantitative measurements. Specifically, we conducted surveys of reviewers in two top-tier double-blind computer science conferences — ICML 2021 (5361 submissions and 4699 reviewers) and EC 2021 (498 submissions and 190 reviewers). Our two main findings are as follows. First, more than a third of the reviewers self-report searching online for a paper they are assigned to review. Second, outside the review process, we find that preprints from better-ranked affiliations see a weakly higher visibility, with a correlation of 0.06 in ICML and 0.05 in EC. In particular, papers associated with the top-10-ranked affiliations had a visibility of approximately 11% in ICML and 22% in EC, whereas the remaining papers had a visibility of 7% and 18% respectively.
“ASAPbio is seeking several new members for our Board of Directors to support our mission to drive positive change in science communication and to broaden our geographic representation.
We are looking for new Board members who can help us deliver on our strategic goals and complement the perspectives of existing Board members. We particularly seek individuals with expertise in the areas below:
Driving and managing culture change
Meta-research, ideally with a strong understanding of the current landscape and trends around preprints and open peer review
Data and information analysis in the context of science communication
We want to increase the geographical representation within the Board, and we would particularly welcome applications from Asia, Europe, Latin America, and Oceania.”
Alberto Pepe, Matteo Cantiello, and Josh Nicholson, in their arXiv paper calling on arXiv to overhaul itself:
Disclaimer: This article has originally been written and posted on Authorea, a collaborative online platform for technical and data-driven documents. Authorea is being developed to respond to some of the concerns with current methodology raised in this very piece, and as such is suggested as a possible future alternative to existing preprint servers.
The paper doesn’t mention that Authorea is owned by Atypon, which itself is a subsidiary of publishing oligopolist Wiley. All three authors are affiliated with the Wiley-owned platform.
Which begs the question: will the arXiv of the future be nonprofit?
Abstract: The arXiv is the most popular preprint repository in the world. Since its inception in 1991, the arXiv has allowed researchers to freely share publication-ready articles prior to formal peer review. The growth and the popularity of the arXiv emerged as a result of new technologies that made document creation and dissemination easy, and cultural practices where collaboration and data sharing were dominant. The arXiv represents a unique place in the history of research communication and the Web itself, however it has arguably changed very little since its creation. Here we look at the strengths and weaknesses of arXiv in an effort to identify what possible improvements can be made based on new technologies not previously available. Based on this, we argue that a modern arXiv might in fact not look at all like the arXiv of today.
Disclaimer: This article has originally been written and posted on Authorea, a collaborative online platform for technical and data-driven documents. Authorea is being developed to respond to some of the concerns with current methodology raised in this very piece, and as such is suggested as a possible future alternative to existing preprint servers.
This study aimed to analyze the content of data availability statements (DAS) and the actual sharing of raw data in preprint articles about COVID-19. The study combined a bibliometric analysis and a cross-sectional survey. We analyzed preprint articles on COVID-19 published on medRxiv and bioRxiv from January 1, 2020 to March 30, 2020. We extracted data sharing statements, tried to locate raw data when authors indicated they were available, and surveyed authors. The authors were surveyed in 2020–2021. We surveyed authors whose articles did not include DAS, who indicated that data are available on request, or their manuscript reported that raw data are available in the manuscript, but raw data were not found. Raw data collected in this study are published on Open Science Framework (https://osf.io/6ztec/). We analyzed 897 preprint articles. There were 699 (78%) articles with Data/Code field present on the website of a preprint server. In 234 (26%) preprints, data/code sharing statement was reported within the manuscript. For 283 preprints that reported that data were accessible, we found raw data/code for 133 (47%) of those 283 preprints (15% of all analyzed preprint articles). Most commonly, authors indicated that data were available on GitHub or another clearly specified web location, on (reasonable) request, in the manuscript or its supplementary files. In conclusion, preprint servers should require authors to provide data sharing statements that will be included both on the website and in the manuscript. Education of researchers about the meaning of data sharing is needed.
AfricArXiv, Eider Africa, eLife, PREreview, and TCC Africa have collaborated to develop a peer-review training workshop, Open Peer Reviewers in Africa, tailored to the region-specific context of African researchers. They co-created tools and strategies for scholarly literature evaluation, and are now ready to pilot the new workshop series with researchers who would be interested in sharing their knowledge by training others, and helping co-develop the resources further.
A debate over claims of room temperature superconductivity has now boiled over into the realm of scientific publishing. Administrators of arXiv, the widely used physics preprint server, recently removed or refused to post several papers from the opposing sides, saying their manuscripts include inflammatory content and unprofessional language. ArXiv has also banned one of the authors, Jorge Hirsch, a theoretical physicist at the University of California, San Diego (UCSD), from posting papers for 6 months.
“In the 10 years since eLife’s inception, we have made significant progress in improving how research in the life and biomedical sciences is communicated. Here we share our vision for a future where a diverse, global community of scientists produces trusted and open results for the benefit of all.
This vision has evolved in response to the changing publishing landscape – namely the increasing popularity of preprints among the life science community, including eLife authors. We are working to achieve our vision in three ways – with the eLife journal, open-source technology development, and our community engagement activities – all of which feed into our overarching ‘publish, review, curate’ mission that puts preprints first.
To succeed in realising our vision, we will:
Continue to develop the ‘publish, review, curate’ model, and encourage its adoption among authors, funders and content curators such as societies;
Build a platform for the ‘publish, review, curate’ model that is open-source, readily adaptable and addresses community needs;
Work with the community of scientists and content curators on new ways to improve the whole research communication process in the ‘publish, review, curate’ world;
And operate a journal for biology and medicine that maintains the highest standards, carries influence in the community and covers its costs….”