Annual Report: 2019 in review

eLife continued to grow throughout 2019, seeing its highest ever volume of submissions and publications. This is a great reminder of eLife’s ever-increasing reputation as “a publisher of outstanding research, innovator in peer review and publishing technology, and advocate for the values of the scientific community,” as our Editor-in-Chief Michael Eisen said when he took on the leadership role in March. The growth we saw in 2019 also allowed us to invest more in new initiatives and experiments to improve the culture of research communication.

We launched a peer-review trial in 2018 that allowed authors, rather than editors, to decide when their paper was ready for publication. We completed the evaluation of this trial in 2019 and reported the outcomes on the Inside eLife blog throughout the year. Overall we found that giving the author the final decision on when to publish their work resulted in a higher proportion of papers being published after revision, although this was balanced out by a higher rate of editorial triage ahead of review.

These results led us to refine our approach to author-led publishing, in particular by switching our focus towards preprints. The new approach, outlined by Michael in a blog post in November, encourages authors to post preprints to bioRxiv and receive eLife peer reviews directly on the preprint, while having their work simultaneously considered for publication in the journal. The eLife editorial decision is only made after all reviews have been obtained, but even if the editor decides the work is not suitable for the journal, the reviews are still posted on bioRxiv so as to be useful to authors, other readers and future journal editors. We piloted this approach towards the end of the year, and the results were encouraging enough to see Preprint Review rolled out more broadly in 2020.

As an accompaniment to this initiative, we have also innovated with our editorial decisions by allowing editors to post summaries of their reasons for accepting a manuscript. Acceptance summaries de-emphasise where the work is published, and instead focus on the reasons why the work is useful. Between Preprint Review and acceptance summaries, eLife is starting to look towards a new future for research communication, where authors control how their work is shared, and journals support dissemination through peer review and endorsement.

In terms of technology, 2019 saw more experimentation and innovation at eLife. We developed a radical new form of research article that allows authors to embed code and data within the manuscript itself, making it executable by readers in real time. The first Reproducible Document Stack (later known as the Executable Research Article) was enthusiastically received by our community, and we have since streamlined the development of these articles to make them available to more authors in 2020.

We also continued to build technology, known collectively as the Libero suite, that serves to underlie our main journal operations, from author submission, XML conversion and typesetting, to the display of published articles. All components of the suite were significantly enhanced over the year, and our aim is to continue to build technology that natively supports the most responsible behaviours in scientific communication. We’re looking forward to some exciting software releases over the coming year.

A central tenet to eLife’s mission is to highlight and promote good practices in the culture of research. Last year, we focused significant attention on improving the geographical and career-stage diversity of our editorial teams and working to balance the gender gap. We have set ambitious targets that we will work towards over the coming years. We also shone a spotlight on key areas of research culture through our Magazine content, for example in articles covering our exploration of mental health in the academic and research sectors – an area that has not received enough attention in the past.

Finally, the year ended with us saying goodbye to eLife’s Executive Director, Mark Patterson, who retired in December. Mark was with eLife from day one, and his vision and oversight helped turn the journal into the thriving success it is today. We are hugely grateful for his leadership and accomplishments at eLife, and will miss him greatly. Damian Pattinson has taken on the baton from Mark. Damian is a long-standing advocate of open-access publishing and a champion of preprints in the biomedical sciences. We are thrilled that he agreed to take on this challenge and excited for him and Michael to guide eLife as we challenge the status quo and strive towards the next generation of peer review and scientific publishing more broadly.

Toby Coppel
Co-Founder and Partner
Mosaic Ventures
Chair, eLife Board of Directors

eLife works across three major areas in support of our mission to transform research communication: publishing, technology and research culture. For the first of these, we aim to publish work of the highest standards and importance in all areas of biology and medicine, while exploring creative new ways to improve how research is assessed and published. The support of the working scientists who serve as eLife’s expert editors is integral to our efforts in this area, and with 2019 came some exciting new appointments to our editorial leadership team, even as we said goodbye to other long-standing members.

In March, we announced Michael Eisen, a leading advocate for open access, as eLife’s new Editor-in-Chief. His outstanding leadership and commitment to reforming research communication for the benefit of scientists and society, as well as his scientific achievements, made him the most appropriate person for this role. He took over from founding Editor-in-Chief Randy Schekman, who stepped down in January to dedicate more time to his role as Chair of the Advisory Council for the Aligning Science Across Parkinson's initiative.

At the end of 2019, we thanked Eve Marder for her service and support as she stepped down from her role as eLife Deputy Editor since April 2015. Before then, she was one of eLife’s founding Senior Editors. Computational neuroscientist Tim Behrens now continues Eve’s work with the Deputy Editors in helping to maintain eLife’s standards for scientific excellence and contributing to policies and processes that ensure fair, constructive and effective peer review.

eLife works to improve the process of peer review so that it more effectively conveys the assessment of our expert reviewers to authors, readers and other interested parties. This ambition is reflected in the transparency of our current process, where anyone can read the peer-review reports and editors' assessment for all published eLife papers. In the future we envision a system in which the outputs of peer review are the primary way research is assessed, rather than journal title.

Results from a new approach

In 2019, we published three sets of results from a peer-review trial where authors could opt into a process in which they had greater control over the ultimate decision to publish. The first report showed that the approach proved popular with authors. There were very similar acceptance rates for male and female last authors, but higher acceptance rates for late-career researchers compared to their early and mid-career colleagues. In the second report, we discussed how the new approach resulted in slightly longer decision times and more appeals against decisions, but several other features of the review process remained unchanged. Finally, the third report showed that the new approach resulted in a moderately higher acceptance rate, with all the issues raised by reviewers addressed by the authors in the vast majority of revised submissions.

As these reports demonstrate, we gained valuable insights into eLife’s regular and trial peer-review processes. By removing the decision to reject after review in the trial process, and by publishing the peer reviews, author responses and editorial ratings, we began to show how the peer-review process does not need to end with a binary outcome of acceptance or rejection, and we started to expose some of its nuances more effectively. We therefore made a plan in 2019 to build upon what we learnt from the trial with upcoming initiatives, detailed below, to show how the results of the review process can be published in an informative way.

New initiatives to enhance the value of peer review

In November, eLife Editor-in-Chief Michael Eisen announced two new initiatives to enhance the value of eLife's peer-review process for authors and the broader community. The first of these, acceptance summaries, involves our editors writing a clear and simple explanation of why a paper was selected for publication in the journal. The second initiative, Preprint Review, offers authors who have posted a paper on bioRxiv the opportunity to have it openly reviewed by eLife on bioRxiv while also being considered for publication in the journal. We published the first acceptance summaries and tested the Preprint Review service with five submissions at the end of the year, and at the time of writing in 2020 have opened Preprint Review up to authors more widely.

All research published in eLife is selected and evaluated by the working scientists and clinicians around the world who serve as our editors. In addition to the scientific content we publish, we give a voice to scientists on broader topics of relevance to them through our Magazine content. We showcase some of the research and feature content that we published in 2019 below.

Philosophers of science have become increasingly interested in biology over the past few decades. While their focus was initially on evolution, the philosophy of biology has now grown to encompass a wide range of areas as this series demonstrates. Following the launch of the collection in March, we published 11 Feature Articles covering topics such as stem cells, immunology, cancer, the microbiome and big data biology.

Our most-viewed paper of 2019 was a Feature Article by eLife Editor Tamar Makin (University College London, UK) and Jean-Jacques Orban de Xivry (KU Leuven, Sweden), titled ‘Ten common statistical mistakes to watch out for when writing or reviewing a manuscript’. At the time of writing in 2020, this article has been viewed more than 110,000 times following its publication in October and was featured in the last eLife podcast of 2019. Meanwhile, a meta-research Feature Article on medical reversals, published in June, has received over 80,000 views and was also highlighted in our September 2019 podcast.

In September, we published a Research Article describing the work of Jessica Meir, a scientist – and astronaut – whose research in physiology has involved riding motorbikes alongside geese as they learn to fly and then investigating how the birds adapt to soar at extremely high altitudes. Jessica’s story, which proved popular among eLife readers and the media when it was published, was also covered in the eLife podcast that same month.

Below are some additional highlights from more than 1,400 research articles published in eLife in 2019.

In a genome-wide study, Timmers et al. developed a scoring system to analyse the variations in our genetic code that influence life expectancy

Image credit: Public domain

Sicard et al. discovered that different segments of a virus genome can exist in distinct cells but work together to cause an infection, potentially reshaping what we know about how viruses infect hosts

Image credit: Sicard et al. (CC BY 4.0)

Strohm et al. described how the eggs of a wasp species protect their food and themselves against detrimental mould fungi by synthesising and emitting gaseous nitrogen oxides that are effective antimicrobials

Image credit: Gudrun Herzner (CC BY 4.0)

A paper by Bhutani et al. revealed how sleep deprivation changes the way the brain processes odours, making us crave high-calorie food

Image credit: Public domain

Yonemitsu et al. described how an infectious cancer spread from one marine mussel to two different species of mussels on both sides of the Atlantic Ocean

Image credit: Susan A. Baldwin (CC BY 4.0)

Ancient DNA analysis by Thomas et al. showed that intense hunting by humans could have caused the rapid extinction of a giant seabird called the great auk

Image credit: Thierry Hubin, RBINS (CC BY 4.0)

A 15-year study by Crispell et al. revealed the genetic clues of the spread of tuberculosis between cows and badgers, with findings that could improve control strategies, reduce disease transmission and cut associated costs

Image credit: Richard Yarnell (CC BY 4.0)

eLife invests heavily in software development, experience design, collaboration and outreach to help realise the full potential of the digital communication of new research. We support the development of open-source tools that can be used, adopted and extended by any interested party to help move towards an ecosystem that serves research as efficiently and as cost-effectively as possible.

In parallel to our in-house software development efforts, the eLife Innovation Initiative is a separately funded effort aimed at providing funding, training and community support for creative individuals and teams within the academic and technology industries. The primary outputs of the Initiative are open solutions aimed at improving the discovery, sharing, consumption and evaluation of research.

Below, we outline a number of developments from eLife’s product, technology and innovation teams in 2019.

In February, we announced the first release of eLife’s open-source submission and peer-review platform: Libero Reviewer. The software takes the form of a wizard that guides authors smoothly through submitting their work for initial assessment by our board of Senior Editors. Designed to save authors time in filling out forms, the tool allows them to simply upload a PDF of their manuscript and the wizard makes use of our open-source extraction technology, ScienceBeam, to lift the manuscript title, abstract and author list directly from the PDF.

Alongside the development of Libero Reviewer, and in conjunction with other members of the open-source community, we continued our work on the extraction of knowledge from PDFs with ScienceBeam. We improved the accuracy of metadata extracted from PDFs, resulting in 95% of titles from uploaded manuscripts being successfully used to prefill forms in Libero Reviewer. Other types of metadata, including the abstract, author names and author affiliations, were also enabled so that we could prefill more fields in the forms, further reducing the time for transforming PDFs into structured data. We hope that as a community-driven effort, we’ll continue to progress rapidly towards making this process as accurate and efficient for authors as possible.

We also made advances in a couple of data science initiatives looking at new topics, such as the taxonomy of peer reviews and how we could more effectively assist our editors in exploring their networks to find the right collaborators for peer-reviewing eLife papers.

In July, we launched the first demo of eLife’s open-source publishing platform: Libero Publisher. This software represents a community-built product based on an in-depth exploration of what publishers both large and small, as well as other organisations, are looking for in terms of a publishing solution. Launching this simple demo allowed us to gather valuable insights from the market and establish a central space to help grow an open-source community focused on building tools for science publishing. This insight and community are helping to inform our current direction and how we build new software for scientists, publishers and other like-minded organisations.

Organised and hosted by the eLife Innovation Initiative, the Innovation Sprint is a global gathering of researchers, developers, designers, technologists, publishers and others to develop open-source prototypes to change the ways we discover, share, consume and evaluate research. Early September 2019 marked the second instance of the eLife Innovation Sprint, where 60 participants worked on 14 projects, from web tools and interfaces to crowdsource research quality indicators, to machine learning tools for topical knowledge extraction.

Tying in with eLife’s work to improve research culture, the eLife Innovation Sprint also represents a valuable opportunity to use technology to elevate researchers and research that are underserved by current systems. Projects from the 2019 Sprint that were developed to help meet this aim include:

• Software Citation – Software citations are important in acknowledging the contributions of software developers and contributors in a traceable manner – yet it is rarely done correctly. The team built skeletons of a web interface that would allow research software developers to generate a citation file and provide and edit rich metadata, and a developer is now turning these skeletons into a minimum viable product as part of the Innovation Leaders programme (detailed below).
  
  
• Inclusion in computational settings – Different computational tools are used by different communities globally, and computational training is offered to increasingly global and diverse audiences. This project aimed to create a resource that crowdsources information and advice on these tools and resources in order to increase inclusivity in computational settings such as training.
  
  
• Hidden Gems – Unintentional biases in mainstream search algorithms can favour preprints with already high visibility, which can be associated with the ‘prestigiousness’ of the senior author and/or their institution, geography, social network reach and so on. Hidden Gems is a prototype platform that aims to counter these biases by shining a light on low-visibility preprints in biology.

Following the Innovation Sprint, we launched eLife Innovation Leaders in October – a new open leadership training and mentorship programme designed for innovators developing prototypes or community projects to improve open science and research communication. Through organising the Innovation Sprint and participating in similar events in the open-science space, we realised that these platforms present excellent opportunities for new ideas, but the projects that start to be developed there can often falter without further support and guidance. With the Innovation Leaders programme, we aim to sustain and maximise the impact of events such as sprints and hackathons, turn ideas into viable solutions, and empower innovators in the community to lead openly.

eLife recognises that reforming research communication depends on improving research culture, and we have invested in research culture in a variety of ways over the years. Our Early-Career Advisory Group has been a guiding force in this, inspiring eLife to establish standards for diversity and inclusion, create peer-support networks, increase early-career involvement in peer review, award grants to early-career authors, and showcase early-career talents and perspectives.

In 2019, we worked to unify our efforts across the organisation and began to define our vision for research culture. Additionally, we:

• Introduced the Ben Barres Spotlight Awards – At eLife, we believe that researchers should not be disadvantaged because of their gender, country of work, career stage, ethnicity or disability. In June, we piloted the Ben Barres Spotlight Awards to provide visibility and collaboration opportunities for scientists from underrepresented groups. Funds were awarded based on the extent to which they would help the recipients and their work, and the first five winners and six runners-up were announced in August.
  
  
• Conducted a survey on mental health in academia – There are growing concerns about mental health in academia, but less is known about the needs of individuals, such as labmates and supervisors, who may be informally supporting those who struggle. This, in turn, limits what can be done to help supportive individuals in this role. To address this, eLife launched a survey that focused on the experiences of people who know (and potentially help) researchers who experience mental health difficulties, and received more than 2,000 responses. The responses are now being analysed with a view to publishing the results later in 2020. This survey is also part of a wider collection of articles that gives a voice to those on the front lines, including group leaders, early-career researchers and non-academic staff.
  
  
• Ran the second eLife Community Ambassadors programme in March – For the second time, we planned to convene and facilitate a worldwide community of like-minded researchers to promote responsible behaviours in science, and we announced 243 Community Ambassadors in April. A post reflecting on their work throughout 2019 included projects that explored science communication and public engagement, the environmental impact of research, and practical steps for increasing diversity in academia. Additionally, the Ambassadors highlighted in a blog post how bullying is an entrenched problem in academia. They now have plans to support victims and launched a survey to learn more about the prevalence and circumstances of such experiences from victims and bystanders. They have also made it easier to keep up with their activities in this area by posting updates under #AcademicAntiBullying on Twitter.
  
  
• Continued our work with the San Francisco Declaration on Research Assessment (DORA) – eLife was a founder of DORA, an initiative that recognises the need to improve the ways in which the outputs of scholarly research are evaluated. In April, we published a blog post describing a DORA workshop that identified a number of ways to reduce bias in hiring and funding decisions. As mentioned in the article, while the group recognises that they are not the first to bring people together for an open dialogue about researcher assessment, they believe (as do we) that such conversations reveal practical intervention points for reform.
  
  
• Held regular webinars on topics of concern to the community and improving culture – On the last Wednesday of each month, members of the eLife Early-Career Advisory Group invite experts to share their views and advice on subjects pertinent to research careers. Reports from each webinar are provided in our #ECRWednesday webinar collection. Just a couple of relevant topics covered in 2019 include ‘Public involvement in research’ and ‘Queer visibility in STEM diversity’.
  
  
• Published other relevant content – Additional Magazine content and blog posts concerning research culture included results from a survey of new PIs in the UK, a discussion of early-career involvement in peer review, and highlights of a workshop convened by the Medical Research Council that gave PhD students the opportunity to discuss how research careers could be made more inclusive for black, Asian and minority ethnic individuals.