Assessment of transparency indicators across the biomedical literature: How open is open?

Abstract:  Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.



Jobs | Microbiology Society | Promotions and Marketing Manager

“The ideal candidate will be a self-starter and be able to think on their feet. They will have solid experience in journals publishing to support the shift in how we communicate and market our journals portfolio. They will also be experienced in designing and delivering campaigns to promote our journals, as well as promote and drive income for our conferences and events. They will possess a high level of creativity, as well as strong marketing knowledge, to primarily help the Society navigate the competitive journals and events environment. This will include understanding the research cycle, Open Science/Open Access, events promotion and the sales process….”

Interview: Cell Genomics

“I am most excited that we are able to publish as a gold open access journal and am grateful to Cell Press for this. It is fitting that we are the first premier research journal to adopt this publishing model, as genomics has pioneered open access. For a field in which the foundation has been based on open access resources and methods, it is essential that the publications are also open access without restrictions, so as to provide broader and more equitable access to this research in ways that drive the progress of science across many fields.

I am equally excited to launch Cell Genomics as an open science journal, providing leadership with best practices in data availability, sharing, and standards. Beyond our publications, we also work with our scientific communities to support open science initiatives in ways that address current challenges and drive progress in genomics and broader scientific research….”

The broken promise that undermines human genome research

“Data sharing was a core principle that led to the success of the Human Genome Project 20 years ago. Now scientists are struggling to keep information free….

So in 1996, the HGP [Human Genome Project] researchers got together to lay out what became known as the Bermuda Principles, with all parties agreeing to make the human genome sequences available in public databases, ideally within 24 hours — no delays, no exceptions.


Fast-forward two decades, and the field is bursting with genomic data, thanks to improved technology both for sequencing whole genomes and for genotyping them by sequencing a few million select spots to quickly capture the variation within. These efforts have produced genetic readouts for tens of millions of individuals, and they sit in data repositories around the globe. The principles laid out during the HGP, and later adopted by journals and funding agencies, meant that anyone should be able to access the data created for published genome studies and use them to power new discoveries….

The explosion of data led governments, funding agencies, research institutes and private research consortia to develop their own custom-built databases for handling the complex and sometimes sensitive data sets. And the patchwork of repositories, with various rules for access and no standard data formatting, has led to a “Tower of Babel” situation, says Haussler….”

INSDC Statement on SARS-CoV-2 sequence data sharing during COVID-19

“The global COVID-19 crisis has brought an urgent need for the rapid open sharing of data relating to the outbreak. Most importantly, access to sequence data from the SARS-CoV-2 viral genome is essential for our understanding of the biology and spread of COVID-19. To aid in that effort, all three INSDC members have prioritized processing of SARS-CoV-2 sequence data and have streamlined the submission process….”

Scientists call for fully open sharing of coronavirus genome data

“Hundreds of scientists are urging that SARS-CoV-2 genome data should be shared more openly to help analyse how viral variants are spreading around the world.

Researchers have posted huge numbers of SARS-CoV-2 genome sequences online since January 2020. The most popular data-sharing platform, called GISAID, now hosts more than 450,000 viral genomes; Soumya Swaminathan, the chief scientist at the World Health Organization (WHO), has called it a “game changer” in the pandemic. But it doesn’t allow sequences to be reshared publicly, which is hampering efforts to understand the coronavirus and the rapid rise of new variants, argues Rolf Apweiler, co-director of the European Bioinformatics Institute (EBI) near Cambridge, UK, which hosts its own large genome database that includes SARS-CoV-2 sequences….”

Apply to join the ASAPbio Board of Directors – ASAPbio

“ASAPbio is seeking two new members for our Board of Directors. With these openings, we aim to 1) improve the racial and ethnic diversity of our board, and 2) include the voice of research trainees, such as graduate students and postdocs. We are also interested in increasing representation from outside the US and beyond cell and molecular biology to include other life science fields.

Both early career researchers and members of minoritized groups hold important, unique perspectives on scholarly communication. For example, transparent and open peer review, concerns about scooping, and publishing biases may be experienced differently by these individuals. We’re seeking vocal people to round out deficits in our current board and help us make productive and equitable decisions about the work we do to make scientific publishing more rapid, open, and transparent. …”

Mandating access: assessing the NIH’s public access policy | Economic Policy | Oxford Academic

Abstract:  In April 2008, the National Institutes of Health (NIH) implemented the Public Access Policy (PAP), which mandated that the full text of NIH-supported articles be made freely available on PubMed Central – the NIH’s repository of biomedical research. This paper uses 600,000 NIH articles and a matched comparison sample to examine how the PAP impacted researcher access to the biomedical literature and publishing patterns in biomedicine. Though some estimates allow for large citation increases after the PAP, the most credible estimates suggest that the PAP had a relatively modest effect on citations, which is consistent with most researchers having widespread access to the biomedical literature prior to the PAP, leaving little room to increase access. I also find that NIH articles are more likely to be published in traditional subscription-based journals (as opposed to ‘open access’ journals) after the PAP. This indicates that any discrimination the PAP induced, by subscription-based journals against NIH articles, was offset by other factors – possibly the decisions of editors and submission behaviour of authors.


An open access dataset for developing automated detectors of Antarctic baleen whale sounds and performance evaluation of two commonly used detectors | Scientific Reports

Abstract:  Since 2001, hundreds of thousands of hours of underwater acoustic recordings have been made throughout the Southern Ocean south of 60° S. Detailed analysis of the occurrence of marine mammal sounds in these circumpolar recordings could provide novel insights into their ecology, but manual inspection of the entirety of all recordings would be prohibitively time consuming and expensive. Automated signal processing methods have now developed to the point that they can be applied to these data in a cost-effective manner. However training and evaluating the efficacy of these automated signal processing methods still requires a representative annotated library of sounds to identify the true presence and absence of different sound types. This work presents such a library of annotated recordings for the purpose of training and evaluating automated detectors of Antarctic blue and fin whale calls. Creation of the library has focused on the annotation of a representative sample of recordings to ensure that automated algorithms can be developed and tested across a broad range of instruments, locations, environmental conditions, and years. To demonstrate the utility of the library, we characterise the performance of two automated detection algorithms that have been commonly used to detect stereotyped calls of blue and fin whales. The availability of this library will facilitate development of improved detectors for the acoustic presence of Southern Ocean blue and fin whales. It can also be expanded upon to facilitate standardization of subsequent analysis of spatiotemporal trends in call-density of these circumpolar species.