bioRxiv & medRxiv; Communicating at the Speed of Science

“Preprint servers bioRxiv & medRxiv have experienced unprecedented growth and attention during these past 18 months as they have contributed to the scientific community’s collaborative response to the present international health crisis. The frequent reports in mass-media outlets alone, after January 2020, demonstrate that bioRxiv and medRxiv are becoming recognized Open Science digital repositories that are at the center of rapidly disseminating scientific research freely throughout the world.

Please join us on Oct 26th at 11am for our inaugural session during Open Access Week 2021 as the Harvard Library welcomes Richard Sever, Assistant Director Cold Spring Harbor Laboratory Press & Co-founder of the preprint servers bioRxiv and medRxiv. Dr. Sever will share his observations and reflections on the exponential growth and impact that preprints have had on advancing scientific communication during this unprecedented time.”

Read & Publish agreement with Jisc – The Company of Biologists

Our two-year cost-neutral Read & Publish agreement with Jisc from 1 January 2020 – 31 December 2021 has been a great success and 29 UK institutions are participating.

We are delighted to announce that we have signed a new three-year Read & Publish agreement with Jisc from 1 January 2022 – 31 December 2024 (with an annual opt out). Information is available on the Jisc website here.

Four key challenges in the open?data revolution – Salguero?Gómez – 2021 – Journal of Animal Ecology – Wiley Online Library

Abstract:  In Focus: Culina, A., Adriaensen, F., Bailey, L. D., et al. (2021) Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub. Journal of Animal Ecology, Long-term, individual-based datasets have been at the core of many key discoveries in ecology, and calls for the collection, curation and release of these kinds of ecological data are contributing to a flourishing open-data revolution in ecology. Birds, in particular, have been the focus of international research for decades, resulting in a number of uniquely long-term studies, but accessing these datasets has been historically challenging. Culina et al. (2021) introduce an online repository of individual-level, long-term bird records with ancillary data (e.g. genetics), which will enable key ecological questions to be answered on a global scale. As well as these opportunities, however, we argue that the ongoing open-data revolution comes with four key challenges relating to the (1) harmonisation of, (2) biases in, (3) expertise in and (4) communication of, open ecological data. Here, we discuss these challenges and how key efforts such as those by Culina et al. are using FAIR (Findable, Accessible, Interoperable and Reproducible) principles to overcome them. The open-data revolution will undoubtedly reshape our understanding of ecology, but with it the ecological community has a responsibility to ensure this revolution is ethical and effective.




The impact of the COVID-19 pandemic on academic productivity

Abstract:  ‘Publish or perish’ is an expression describing the pressure on academics to consistently publish research to ensure a successful career in academia. With a global pandemic that has changed the world, how has it changed academic productivity? Here we show that academics are posting just as many publications on the arXiv pre-print server as if there were no pandemic: 168,630 were posted in 2020, a +12.6% change from 2019 and +1.4? deviation above the predicted 162,577 ± 4,393. However, some immediate impacts are visible in individual research fields. Conference cancellations have led to sharp drops in pre-prints, but laboratory closures have had mixed effects. Only some experimental fields show mild declines in outputs, with most being consistent on previous years or even increasing above model expectations. The most significant change is a 50% increase (+8?) in quantitative biology research, all related to the COVID-19 pandemic. Some of these publications are by biologists using arXiv for the first time, and some are written by researchers from other fields (e.g., physicists, mathematicians). While quantitative biology pre-prints have returned to pre-pandemic levels, 20% of the research in this field is now focussed on the COVID-19 pandemic, demonstrating a strong shift in research focus.

Register for the ORION Open Science Final Conference 27-28 September | ORION Open Science

“Welcome to the virtual final ORION Open Science Conference on 27-28 September to learn about and discuss achievements and lessons learned throughout the ORION project from 2017 to 2021. The conference is free of charge and open to anyone interested in Open Science and RRI practices, and its future national and international implications.

At the heart of the ORION Open Science EU-project is the ambition to open up the way we fund, organise and conduct life science research. During the project lifetime we have developed and tested a wide range of engagement methods, funding schemes, training materials and co-creation activities to engage the public in science. Now it is time to open up and share with you our achievements, tools and lessons learned. …”

Why I am building Arcadia.

“I walked away with the backing to establish a new startup, Trove….

At Trove, we are led by curiosity and remain committed to learning and sharing the knowledge we’ve gained. There is no need to lock up the lessons we’ve learned from others in the tick community. In fact, we have sought their feedback, and we will publish most of our protocols, tools, and datasets without paywalls or delays. It’s the most rigorous any of us have ever had to be, and all of this is in the absence of journals. Our work may ultimately translate into products that could be useful to many more people….

For all these reasons, I have decided to take the best parts of my experiences to build a new research organization called Arcadia Science. I am co-founding Arcadia with yet another fierce woman scientist Prachee Avasthi, who is a leader among leaders in the fight for open science. …”

Motivations, concerns and selection biases when posting preprints: a survey of bioRxiv authors | bioRxiv

Abstract:  Since 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors’ biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find weak evidence that authors preferentially select their highest quality, most novel or most significant research to post as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.


WUR gives away CRISPR intellectual property licenses for free in fight against hunger – Reader Mode

“The ultimate aim of plant breeding has always been to make plants resistant to drought and diseases. That could help eliminate hunger around the world. This is no longer a distant thought, thanks to a technology called CRISPR-Cas. Today Wageningen University & Research (WUR) announces it will provide potential partners with free licenses to work on its patented CRISPR technology. The license must be applied to gene-editing of plants for non-profit applications….”

WUR gives away CRISPR intellectual property licenses for free in fight against hunger – Reader Mode

“The ultimate aim of plant breeding has always been to make plants resistant to drought and diseases. That could help eliminate hunger around the world. This is no longer a distant thought, thanks to a technology called CRISPR-Cas. Today Wageningen University & Research (WUR) announces it will provide potential partners with free licenses to work on its patented CRISPR technology. The license must be applied to gene-editing of plants for non-profit applications….”

NSF-funded, Husker-led project to evaluate open-access educational resources | Nebraska Today | University of Nebraska–Lincoln

“So the landmark NSF report called on educators to prioritize conceptual understanding over facts, emphasize the scientific process as much as the result, and explore ways to give students a greater stake in their own learning. Even before the report, but especially in the decade after, instructors developed so-called open educational resources — freely available lesson plans, lab activities, quizzes and other course materials — to help incite the instructional revolution.

With the support of a nearly $2 million grant from the NSF, Couch is now leading a five-year, multi-institutional effort to gauge the creation, evolution and implementation of those open educational resources….”

B2X – a new pipeline for author services

“For several years, bioRxiv has made life easier for authors by enabling them to send their papers directly from bioRxiv to journals. This B2J (bioRxiv-to-journal) technology saves people time by automatically transferring their PDF, metadata and any source files to journal submission systems so they don’t have to upload these again at the journal website and re-enter all the information. Around 200 journals now participate in B2J, and portable peer review services such as Review Commons also participate.

We are now introducing a new delivery pipeline – B2X – that will enable authors to send their manuscripts to a variety of third-party services. These services are completely independent of bioRxiv and may include groups that assess particular aspects of manuscripts, help authors improve them, or check for compliance with specific funder requirements. The first organization to join B2X is DataSeer, a service that helps researchers navigate open data policies.

DataSeer scans articles for datasets collected and provides recommendations for how these should be shared. Authors receive a brief report on the data that should be shared and advice on metadata, file formats, and appropriate repositories. They can also obtain an Open Data certificate documenting data deposited in public repositories….”

Read & Publish agreement with CSIC | The Company of Biologists

“The Company of Biologists is pleased to announce a new Read & Publish agreement with the Spanish National Research Council.

This cost-neutral agreement, which runs until 31 December 2023, enables researchers at more than 100 Consejo Superior de Investigaciones Científicas (CSIC) institutes to publish an uncapped number of Open Access research articles in Development, Journal of Cell Science and Journal of Experimental Biology at no cost to them. They will also benefit from free and unlimited access to the journals and their archives dating back to 1853….”

Digital sequence information: free access is crucial | Leibniz Institut DSMZ

Global problems such as the extinction of species and the decline of biological diversity, climate change, pandemics and hunger can only be solved with free access to digital sequence information”, states Prof. Jörg Overmann PhD, Scientific Director of the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures. “Without free access to digital sequence information [DSI], research on a national, European or international level will simply fail to work. Digital sequence information must be preserved as common good”, stresses Prof Overmann. 

NIH-Wide Strategic Plan: Fiscal Years 2021-2025

“NIH is committed to making findings from the research that it funds accessible and available in a timely manner, while also providing safeguards for privacy, intellectual property, security, and data management. For instance, NIH-funded investigators are expected to make the results and accomplishments of their activities freely available within 12 months of publication. NIH also encourages investigators to share results prior to peer review, such as through preprints, to speed the dissemination of their findings and enhance the rigor of their work through informal peer review. A robust culture of data sharing is critical to continued progress in science, maximizing NIH’s investment in research, and assurance of the highest levels of transparency and rigor. To this end, NIH will continue to promote opportunities for data management and sharing while allowing flexibility for various data types, sharing platforms, and strategies. Additionally, NIH is implementing a policy requiring that all applications include data sharing and management plans that consider input from stakeholders….”

?Clarivate?Acquires?Bioinfogate, Reinforcing Position as Premier Provider of End-to-End Research Intelligence Solutions for Life Sciences – Clarivate

“?Clarivate Plc?(NYSE:CLVT), a global leader in providing trusted information and insights to accelerate the pace of innovation, today announced that it has acquired Bioinfogate, a leading provider of analytics solutions in the life sciences and producer of the OFF-X™?portal.?Financial terms of the transaction were not disclosed.

The?Bioinfogate?OFF-X™?portal is a cutting-edge safety intelligence solution aimed at empowering pharmaceutical organizations to identify toxicology and safety signals, mitigate safety liabilities and de-risk early-stage assets. It is one of the largest?translational safety and toxicity?portals, featuring over 1,200,000 safety alerts corresponding to over 23,000 drugs and biologics and more than 15,000 targets of pharmacological interest….”