Annual Report: 2018 in review

We reflect on eLife’s achievements in continuing to improve peer review, transforming technology for academic publishing, and supporting communities for open science.
Inside eLife
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Letter from the Chairman

At the core of eLife’s mission is the goal to support a shift in research culture towards greater cooperation and transparency in science. In 2018, eLife took a number of important steps directed towards this goal.

Chief amongst these efforts were those to build stronger connections with the early-career research community, beginning in January with the appointment of a new member to eLife’s Board of Directors. Prachee Avasthi has been a faculty member at the University of Kansas Medical Center for nearly four years. Since joining the Board at eLife, she has contributed immensely to eLife's work, not least by serving on the appointment committee, which led to the recruitment of our new Editor-in-Chief, Michael Eisen. Another initiative geared towards the early-career community was the launch of the eLife Ambassador programme in 2018. In addition, we replenished the Early-Career Advisory Group and started an effort to engage more early-career researchers in peer review and in the editorial board. All of this work is borne from the conviction that the cultural change we seek will be impossible without the creativity, energy and brilliance that is so evident amongst graduate students, postdocs and early independent researchers, but is often stifled by the current hierarchical structures and incentive systems that operate in academic science.

Alongside our work with the research community, we initiated a trial of a new peer-review process that gives authors greater control over how they respond to comments after peer review. The trial received strong support as well as some criticism from the community, and as we entered 2019 we shared the first results. As we iterate our trials to improve scientific communication, we are comforted by the robust support for the idea that such experiments need to be conducted and the results communicated, so that new approaches to publishing can be developed.

The editorial side of eLife also developed considerably with the introduction of a new section covering the Physics of Living Systems, the division of some of the existing sections into new sections, and a major collection of articles on mechanisms in microbiome research. To give greater prominence to the non-technical summaries that are provided for many of the research articles, we introduced the Science Digest section of eLife. Beyond the outstanding research that we published at a rate of over 100 articles per month, we created content collections on meta-research and scientists as parents, to serve the scientific community in ways that go beyond publication of regular research articles.

The transition towards open science will be catalysed to a great extent by new technology and products that are geared towards these practices. To that end, eLife continued to invest heavily in open infrastructure and technology innovation. Together with several like-minded partners we have created an open-source community with the ambitious aim to build shared infrastructure, designed to support a range of publishing workflows. The work is already bearing fruit as components of the system are steadily being launched by eLife and our partners. In a related project, eLife’s collaboration with Hypothesis was completed in 2018 with the launch of open annotation tools that are now being used by many other publishers. In all this work the emphasis is placed on modes of research communication that align with open science, including open access. Success will then be judged by the extent to which these products are used to support a transition towards greater access and openness.

Shortly after 2018 drew to a close, the staff, editors and board of eLife were able to pay tribute to the founding Editor-in-Chief of eLife, Randy Schekman, who stepped down in January 2019. As Randy’s successor, the board was delighted to appoint and welcome Michael Eisen (Professor of Molecular and Cell Biology, University of California, Berkeley) to build on the strong foundation that Randy has created. For 20 years, Michael has led by example in his efforts to promote open science, and in his first few months at eLife he has already developed strong relationships with staff and the editors and is identifying the next steps we need to take for eLife to catalyse the continued reinvention of research communication. We are looking forward to working with Michael so that eLife can take even greater strides towards our vision to help accelerate scientific discovery.

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

Continuing to improve peer review

At eLife we are keen to explore potential improvements to all aspects of scientific publishing – especially peer review. While thousands of authors and referees have experienced our consultative approach to providing feedback to authors, in 2018 we experimented with a new process. We also participated in research into potential bias in the editorial process.

Trialling a new approach

Building on ideas presented by Erin O’Shea and Bodo Stern, in June 2018 eLife conducted a trial whereby we committed to publishing the author’s submission if the paper was invited for in-depth review – together with the decision letter, peer reviews and author response. In the trial, papers that were encouraged for peer review would also be published with a statement summarising the Reviewing Editor’s assessment of the revised submission. The statement would indicate that the authors had addressed all the issues, or whether minor or major issues remained unresolved.

There were 313 submissions to the trial process, with 70 encouraged for in-depth review. We have been comparing the outcomes of these papers with 665 regular submissions that we received during the same period. We have started to report the results of the trial (see Peer review: First results from a trial at eLife), and further data will be released in 2019. Based on the outcomes we will modify our processes, conduct further trials and share our findings so that others can also benefit from and build on our experiences.

Promoting fairness and diversity

In 2018 two eLife Reviewing Editors, Cassidy Sugimoto and Jennifer Raymond, collaborated with colleagues to investigate whether decision outcomes differ between male and female authors, and for authors from different countries. Our aims were to better understand any disparities, to share data of interest to others, and to try and improve our own process. A preprint by Murray et al. suggests that the acceptance rate for papers with male last authors was slightly higher than for female last authors. On the other hand, it appears that decision outcomes are more equitable when the pool of reviewers and editors is mixed-gender. The study is prompting us to improve the diversity of our editorial board and other communities, and to consider other trials where we can explore the disparities in decision outcomes further.

Early-career involvement in peer review

We want to ensure that early-career researchers are involved in peer review – as referees and as members of our editorial board. In 2018 our editors initiated a one-year trial in which a group of editors committed to include an early-career researcher in the review process for papers they handled in the areas of genomics and evolutionary biology. We will provide feedback on our experiences in 2019.

From the eLife journal

eLife’s reputation is built on the quality of the content that we publish. The eLife editors select and peer review work that they judge to be particularly valuable for their field. We also publish articles and interviews with researchers about broader issues relevant to science, to raise awareness of some of the cultural changes that we and our funders would like to influence. Below we provide some highlights of the broad scientific content from eLife in 2018, as well as some of the additional feature content.

A new section – The research articles in eLife are classified into major subject areas, and in 2018 we introduced a new subject to highlight research work that intersects physics and biology. The launch of the Physics of Living Systems section was led by Senior Editor Arup Chakraborty, and in 2018 included research covering topics including morphogenesis, mechanosensation and membrane curvature, as well as an essay on theory papers which was accompanied by the shortest abstract we have ever published.

A special issue – Another first in 2018 was to publish a special research issue, in this case focused on the topic of mechanistic microbiome research. Led by Senior Editor Wendy Garrett, a group of editors have selected 13 peer-reviewed articles for the issue to date including an article about how the order in which bacteria colonise the gut has a big influence on the eventual microbiome. This collection of articles has stimulated the submission of further first-rate research on this important topic.

Collection on meta-research – Research about the research process itself is becoming increasingly important as funding becomes tighter and the attention on research outcomes increases. Over the years, eLife has published many widely read articles in this field. To signal our growing interest in the topic, we brought all of the relevant articles together in a collection towards the end of 2018.

Parent-scientists – Highlighting the challenges faced by many scientists with dependents, we published a large collection of interviews on this topic. The stories of the researchers featured in the collection highlight how making research more ‘family-friendly’ could benefit all scientists and might help to counteract the lack of flexibility and intense competition that researchers often experience.

Here is a small selection from more than 1,200 research articles that eLife published in 2018:

A paper by Zhang, Li et al. described pigs that were genetically modified to digest more nutrients from their feed, as a potential step towards helping reduce the pork industry’s carbon footprint.

Image: Pig, by Nick Saltmarsh (CC BY 2.0)

Minhas, Bawdon et al. revealed how a type of bacteria causes body odour, paving the way for future studies that could help uncover new ways of tackling this problem.

​​​​​

In our newest subject area, the Physics of Living Systems, Frangipane et al. reported the use of light patterns to control the swimming speed of Escherichia coli bacteria and direct them to form different shapes, in a move that could inform the next generation of microscopic devices.

Image: Frangipane et al. (CC BY 4.0)

A study by Troup et al. reported the use of optogenetics to reveal a larger role for the fly brain 'sleep switch' neurons in controlling both waking and sleeping behavioural responsiveness.

Image: Fruit flies at rest, by Jim McLean (CC BY-NC-SA 2.0)

Souza, Moreno-Letelier et al. identified the Cuatro Ciénegas Basin in Mexico as a true ‘lost world’ – a safe haven where ancient microorganisms found refuge and have kept evolving.

Image: Valeria Souza (CC-BY 4.0)

In a cancer study, Smith and Sheltzer found that gene copy number provides more prognostic information than gene mutation status, which, if confirmed on a different set of data, could inform the development of new technologies to introduce this approach in the clinic.

Fu et al. described how a fossil plant species, which they called Nanjinganthus, suggests that flowers bloomed in the Jurassic of China – almost 50 million years earlier than previously thought.

Image: Takayuki Miki (CC BY-ND 2.0)

Transforming technology for academic publishing

Last year we announced our intent “not just to provide the best experience we can for eLife’s own journal, but also to make tools that others can use, engage with and contribute to”. We envisage a common infrastructure for research communication that publishers can leverage to save money and time – which can then be better spent on new challenges. In 2018 we took, along with several organisations and partners, some important steps toward an end-to-end open-source infrastructure for academic publishing.

Libero Publisher: A modern approach to presenting research online

There are many lessons to take from the established open-source technology development community: to make software open-source is not the same as making it reusable for another organisation; open-source technology requires strong and persistent oversight; and the long-term use and health of open-source tools demands a high level of community involvement. We took each of these lessons on board in 2018 with the re-introduction of Libero Publisher. First released as the open-source version of the technology behind the eLife journal site today, Libero Publisher is being rebuilt in consultation with other academic publishers to make it usable for other journals and publications both within and outside the life sciences. While we are borrowing heavily from the eLife journal platform, including the extensively tested user-centered design, we have revisited the core underlying data model to more easily accommodate other content providers’ requirements for what’s included in the published article. Much of 2018 was spent defining the core of a common content exchange system, and the first usable release is expected in the summer of 2019.

Libero Reviewer: Community-driven infrastructure for submission and peer review

In parallel with community efforts around Libero Publisher, we’ve seen success in shared infrastructure with Libero Reviewer and the Coko Community. A joint effort in designing and building reusable components saw the launch of Hindawi’s new reviewer application in October 2018. At the time of writing in 2019, the submission systems for Europe PMC and eLife have also now been released. All the applications are built on the same codebase and supported by the community.

Setting standards for content access and reuse

One of the keys to adopting common infrastructure and avoiding redundant effort in publishing is establishing agreement around how content should be classified, organised and made available. eLife has contributed to many efforts to this effect, including JATS4R (recommendations for standardising JATS XML) and the Validator Tool, Metadata2020, FORCE11, CrossRef, the Initiative for Open Citations (I4OC) and the NISO Manuscript Exchange Common Approach (MECA) working group.

Hypothesis: Investing in tool development for common use

In 2018 we announced the outcomes of our partnership with Hypothesis, an open-source tool for open annotation on the web. The promise of open annotation for advancing scholarly discourse online is exciting, and scholarly publishers are uniquely positioned to try and encourage this as centres for community engagement and interaction around new research. Through our partnership, Hypothesis developed moderation features, single sign-on authentication and user interface customisations that give publishers more control over its implementation on their sites. As a result, a wide range of publishers and hosting platforms have integrated the tool or are using it in their workflows, including: Highwire, Atypon, the Public Knowledge Project’s Open Journal Systems, American Diabetes Association, Cambridge University Press, University of California Press, and many others. This is exactly the kind of tool reuse that eLife aims to make possible.

Fastly: Using the latest tools to accelerate content delivery

An important shift on the technology side in 2018 was our move to a new content delivery network named Fastly. Thanks to this move, journal pages are loaded from “edge networks” located closer to our readers. This helps pages load more quickly, especially in areas with slower internet infrastructure or for those readers further away from our cloud provider’s servers. Fastly also provides a shield to our own infrastructure, resulting in a more secure and robust platform with defence from cyberattacks.

Convening and supporting communities

A central theme to eLife’s work to date has been to participate in, build and support communities that promote responsible behaviours in research. Whether these are communities of early-career researchers, open-science advocates or like-minded publishers, eLife is providing different types of support to help them take root and thrive.

Increasing our engagement with early-career researchers

2018 saw the launch of the first eLife Ambassadors programme led by Emmanuelle Viré, a group leader at University College London (UK), who has served for several years on eLife’s Early-Career Advisory Group. The programme attracted more than 200 scientists, mostly graduate students, postdocs and early group leaders, from six continents and was intended to support grass-roots projects identified by the ambassadors themselves. It has been heartening to witness the enthusiasm and commitment this group brought to a range of initiatives covering preprints, reproducibility, diversity in science, peer review, mentoring and much more. The ambassadors also created their own blog – ecrLife – and a resource about early-career funding. Having learned many valuable lessons in 2018, we have recently launched the second Ambassador programme, which is quickly picking up momentum.

In January, eLife announced the appointment of Prachee Avasthi to the eLife Board of Directors, the highest level of governance in the organisation. Prachee has been a group leader at the University of Kansas Medical Center for just under four years. Already Prachee is bringing perspectives to the Board discussions that are contributing in important ways to the direction we are taking as an organisation.

In many ways, it was the appointment of the inaugural Early-Career Advisory Group in 2014 that was the catalyst for closer engagement with this community. In 2018 we conducted a second annual election to replenish five members of the group, selected from over 100 applications.

The inspiration for all of our initiatives with early-career researchers is that we will never achieve the kind of cultural change that supports greater transparency and collaboration in science unless we involve those who are most committed to seeing this change happen... We sincerely hope that other organisations, especially funding agencies and research institutions, take similar steps.

The inspiration for all of our initiatives with early-career researchers is that we will never achieve the kind of cultural change that supports greater transparency and collaboration in science unless we involve those who are most committed to seeing this change happen. And as we work more closely with the early-career community, this approach is only being reinforced by our experiences. We sincerely hope that other organisations, especially funding agencies and research institutions, take similar steps. There is massive untapped creativity and energy within this group, which organisations will benefit from. The early-career researchers who are given these opportunities will also gain from the experience by building the reputation they need to support their future careers.

Encouraging broad approaches to assessment and recognition: DORA

As well as promoting grass-roots efforts that support improvements in the communication and evaluation of science, eLife is advocating for change in policy and practice. Nowhere is this change more needed than in the area of research evaluation. eLife was one of the organisations that helped launch the San Francisco Declaration on Research Assessment (DORA) and five years later, in 2018, eLife helped to reboot DORA. Along with six other organisations, eLife helped to launch a new website, establish a steering committee, and most important of all, recruit a community manager to drive the initiative forward. DORA has gained much momentum as a result and continues to be highlighted by high-profile initiatives including Plan S, which was also announced in 2018. One of the most important new areas of work for DORA is to gather examples of good practices in research evaluation, to demonstrate that these practices are steadily moving away from research evaluation based on journal brands, towards more meaningful and fairer approaches that take a broader range of contributions into account. It is only when we change what we value in science in this way that we will achieve the change in behaviours that we and others are striving for.

Channeling the community’s energy into creating new tools for discovery

One of the most memorable events of 2018 was a two-day innovation sprint that eLife hosted in Cambridge, UK, in May. Around 60 participants – researchers, developers, designers, publishers – gathered and self-organised into small teams to work on more than a dozen ideas related to improving science. The event was an uplifting, collaborative and productive experience for everyone involved, and participants have pointed out the parallel between the practices adopted at this event and those that many of us would like to see valued in science itself. Plaudit, a browser extension to allow scientists to share research recommendations, and SwipesForScience, a templating service that lets researchers create mobile-friendly games for analysing large amounts of research data, were two of the projects explored at the sprint which were subsequently funded by eLife for further development.

Financial summary

Analysis of revenue

Publication fee income increased by 75% over 2017 as almost all articles published this year were subject to a fee, whereas many of the articles published last year had been submitted before we introduced publication fees.
Grant income has also increased in 2018 as a result of an additional funder, the Knut and Alice Wallenberg Foundation, which is specifically supporting our technology and innovation work.

Analysis of expenditure

Our technology and innovation expenditure has grown by 35% relative to last year, as reflected by the level of activity described above. Publishing costs changed very little, and so technology and innovation spending has increased from 30% of total expenditure last year to 37% in 2018.
Within the publishing costs the proportions of major spending areas are broadly the same as in 2017.

As a result of the timing of grants received, we reported a surplus before tax of £464,000 in 2018 compared to a deficit of £257,000 in 2017.

Revenue and expenditure, years ended December 31 2018 and 2017 (in £ thousands)

Revenue20182017
Grants4,2903,832
Publication fees2,1551,233
Total6,4455,065
   
Expenditure20182017
Publishing3,7953,708
Technology and innovation2,1861,614
Total5,9815,322
   
Surplus/(deficit) before tax464(257)

We claim grants from our funders in advance, based on our expected expenditure, and our actual expenditure often differs from this slightly. This can result in us reporting a surplus or deficit in individual years. This can be seen in the graph below, which also shows that in spite of the deficit in some years, we generally have total reserves in the range £0.2–0.6m.

The full audited accounts for eLife Sciences Publications, Ltd for 2018 are available below. As a US-registered tax-exempt organisation, we also publish detailed financial information in our Form 990.

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