Events – ASAPbio

Empowering Researchers: Leveraging Preprints for Academic Advancement

ASAPbio — Thu, 04 Apr 2024 00:00:00 +0000

Guest post by; Doherty Funmilayo PhD, Atoyebi Abdulwakeel O., Balogun Peter, Aguh Anthony and Adamolekun Emmanuel

A hybrid training titled “Empowering Researchers: Leveraging Preprints for Academic Advancement” was organized by Yaba College of Technology, Centre for Research Support and Grants Management, Lagos, Nigeria on March 11, 2024 and sponsored by ASAPbio as one of their community projects. The significant event brought together participants in research, and academia, both physically and virtually, to unlock the transformative potential of preprints – a revolutionary tool that promises to accelerate the dissemination of knowledge and foster collaboration.

The event kicked off with leading experts taking the stage to demystify the world of preprints. From defining their very essence to debunking myths and addressing concerns, the presentations left no stone unturned, equipping attendees with a comprehensive understanding of preprints.

The interactive workshop allowed participants to immerse themselves in the practical aspects of preprint submission, open peer review, and navigating the intricacies of preprint repositories. These hands-on sessions empowered researchers with the skills to harness the full potential of preprints, ensuring they remain at the forefront of academic advancement.

In her welcome address, the Acting Director of Centre for Research Support and Grants Management, Dr. Funmilayo Doherty, shed light on the event’s pivotal objective: to create awareness about preprints, a concept that has yet to thrive and be fully embraced in Nigeria. Her words resonated deeply, underscoring the urgency to embrace this transformative tool and unlock its vast potential for the continent’s research endeavours.

In a call to action, the Rector of Yaba College of Technology, Dr. Engr. Ibraheem Adedotun Abdul, urged researchers in tertiary institutions to embrace preprints wholeheartedly. He painted a vivid picture of a future where knowledge is democratized, inclusivity and transparency reign supreme, and collaboration transcends boundaries.

In his opening remark, Jonny Coates, the Associate Director at ASAPbio, set the tone for the event. With insightful remarks, he laid the foundation for the discussions ahead, emphasizing the importance of preprints in transforming academic research. Coates’s words resonated deeply, igniting a sense of anticipation for the enlightening sessions to come.

The event witnessed a remarkable turnout, with 53 virtual attendees, 74 physical attendees (including researchers from Yaba College of Technology and the University of Lagos), and a staggering 278 registered participants – a testament to the growing recognition of preprints as a catalyst for academic excellence.

Among the esteemed speakers was Godwyns Onwuchekwa, Head of Community at eLife, who illuminated eLife’s new publishing model utilizing preprints and the invaluable lessons learned along the way. He delved into topics like the benefits of using preprints, eLife’s approach to actively engaging with them, and insights into the future of academic publishing.

Harold Bowa from UbuntuNet Alliance captivated the audience with his comprehensive introduction to preprints – explaining what they are, how they differ from journal publications, and emphasizing their essence in accelerating rapid knowledge dissemination. Bowa also highlighted preprints’ vital role in fostering early collaboration among researchers by inviting feedback from peers before formal peer review. His myth-busting insights addressed common concerns surrounding preprints as well.

Jonny Coates, Associate Director at ASAPbio, provided an overview of the resources and opportunities offered by ASAPbio to support preprint adoption.

Vanessa Fairhurst, Community Manager at PREreview, introduced the audience to the PREreview platform, explaining why reviewing preprints is important in the context of models like the Preprint Review Club (PRC), and even gave a walkthrough demo on posting reviews to PREreview.

As the curtains closed on this significant event, it became evident that a major shift had begun – a shift that promises to propel African research onto the global stage, shattering barriers and ushering in a new era of academic innovation. The “Empowering Researchers: Leveraging Preprints for Academic Advancement” event was not just a gathering; it was a clarion call, a catalyst for change, and a testament to the unwavering pursuit of knowledge that defines the African research community.

The positive reception was palpable, with participants expressing their appreciation for the event and its potential to transform research practices:

“As an early career researcher, I found this event incredibly eye-opening,” shared one participant. “The presentations and workshops demystified preprints in a way that made me feel empowered to start utilizing them in my own work. I’m excited about the possibilities for accelerating the dissemination of my research findings and fostering valuable collaborations through preprint platforms. The hands-on training was invaluable.”

Another attendee, who initially had reservations about preprints, stated, “This event addressed my concerns comprehensively. The expert speakers provided a balanced perspective, highlighting both the benefits and potential challenges. I’m now convinced that preprints are a vital tool for enhancing research visibility and promoting open science practices. The panel discussions were thought-provoking and gave me a deeper appreciation for the future of academic publishing.”

A senior researcher, who has witnessed the traditional publishing landscape evolve over the years, expressed, “This event opened my eyes to the transformative potential of preprints in a way I hadn’t fully grasped before. The organizers did an excellent job of creating a supportive environment for participants to learn and engage with this emerging trend. I’m inspired to explore preprint platforms and encourage my colleagues and students to embrace this innovative approach to knowledge dissemination.”

Media outlets have covered the event. Reports from newsflasher and newmail highlight the significance of the discussions and the urgency conveyed by participants and speakers alike. This widespread coverage underscores the event’s impact in catalyzing a transformative shift in academic research practices, not only in Africa but on a global scale. You can watch the event on YouTube (part 1 & part 2).

The trials and tribulations of post publication peer review; Recap from November Community Call

ASAPbio — Mon, 11 Dec 2023 00:00:00 +0000

In our November 2023 community call, we heard from Lonni Besancon (Assistant Professor, Linkoping University) about his work exposing fraudulent and unreliable science.

Lonni began with an overview of how he started researching reliability issues and highlighted that this is not his primary role; indeed, it is a large issue in the current system that there are few full-time positions focussed on quality checking the scholarly literature. Lonni described how this quality checking was particularly important during COVID-19 pandemic and how he and others identified COVID-19 work that was potentially problematic, including by looking at the time between submission and acceptance. Lonni also drew attention to the large number of these problematic articles which were published in journals in which the authors held editorial positions. This clear conflict of interest was a key theme throughout the discussion.

Lonni pointed to two useful resources for problematic papers; retraction watch for news and tracking retracted work and PubPeer for posting comments of concern on papers. Lonni also discussed the issues with getting problematic work retracted by journals and used examples of papers he had worked to get retracted as examples. Worryingly, many of these problematic papers Lonni highlighted had very high altmetric scores and were cited/read considerably more than the average article.

During his talk, Lonni used a number of examples including one of a retraction that was an open science success story, as the authors had shared their data openly, which enabled the community to discover issues with the analysis. Lonni also provided an example where a journal was reluctant to publish a rebuttal and highlighted that this is a larger issue. In this case, the editor of the journal refused to publish the rebuttal as it “did not encourage debate in scientific discussion” by calling for the problematic article to be retracted.

In addition to identifying problematic papers based on methodology or results, Lonni highlighted that there is a large issue around inappropriate use of citations that misrepresent the literature. In particular, Lonni described his most recent work that revealed manipulation of citations by a publisher – a worrying practice if this is more widespread. Lonni summarised his talk by reinstating the importance of correcting the scientific literature and that there should be an error-checking culture. However, until we provide credit for this kind of work, that desperately needed culture wont grow. We also need to collectively combat the conflicts of interest that publishers and institutions have regarding retracting work; Lonni ended by saying that many editorial staff and publishers are not helpful in retracting bad science.

Lonni’s talk provided a great introduction to an active discussion that followed. The discussion began by focusing on the personal story Lonni had told and how much of a toll this takes. Lonni pointed out that it was tough in the beginning as he felt alone in performing this kind of work. However, as he discovered others this got better and is now a strength. Lonni stated that the death threats no longer affect him too much as he sees these as remaining online but that the professional and legal attacks are much more difficult to handle. There are concerns around whether the universities would be supportive and there is a large financial cost to the researchers who quality check the scientific literature.

When asked where we should be devoting energy and resources to correcting things, Lonni highlighted the immediacy of the COVID pandemic and the importance of focussing on research with an impact on society. Tied to this, potentially problematic papers could be flagged by reviewers (e.g. through normal peer review or through initiatives like PREreview) or on PubPeer or through screening tools like the Problematic paper screening tool which looks for “tortured phrases” in papers.

One participant posed that a potential solution may be in micropublications which may help increase the chances of researchers detecting issues before a full paper is published. Additionally, providing much higher resolution images would reduce the potential for problematic papers.

As researchers, how do we feel about the involvement of the legal system? Publishers and data sleuths often face threats of legal action for retracting work which is causing irreparable harm to correcting the scientific literature. Is the answer in micropublication and producing higher resolution images with a credited researcher? Or does academia need a regulatory body, as so many other industries have had for quite some time?

If you missed the conversation you can catch a recording here https://www.youtube.com/watch?v=gECAVqafQgg.

Community and commercialisation in biomedical preprint servers

ASAPbio — Wed, 08 Nov 2023 00:00:00 +0000

Science is a community effort, but publishing has long been co-opted by commercial interests, where researchers’ labor in authoring, reviewing, and editing are used to bolster publishers’ profits. Preprints are free to post and read, but to what extent do commercial interests influence the space? The theme of Open Access week 2023 was “community over commercialisation” and ASAPbio hosted an event investigating this theme in biomedical preprint servers.

In some fields preprints have been a staple since the 1990’s whilst in others preprints remain relatively obscure. Despite this, there are now over 50 preprint servers ranging from field or country-specific to general servers. Each server has their own approach to governance, funding and features. Some preprint servers are community orientated whilst others are owned and operated by publishing companies. In fact, the largest biomedical preprint server in terms of monthly volume is Research Square, which has close ties to Springer Nature. It is vital that we hold conversations around how preprint servers are controlled to ensure that the publishing industry does not co-opt preprints as has occurred with many facets of open access.

Do preprint servers align to open principles?

The event opened with a talk by ASAPbio board member and consultant, Jennifer Lin. Jennifer began by looking at the trends in preprint posting across servers since 2019, highlighting that some servers had actually contracted in recent years whilst others have grown, although none had grown as much as they had during the COVID-19 pandemic.

Jennifer reiterated the theme of open access week, stating that the UNESCO recommendation on open science calls to prioritise community over commercialisation. Jennifer highlighted that often, commercial (financial stakeholder) interests are prioritised over community needs by owners of commercial entities and that there is a cost to this; primarily the erosion of trust.
Jennifer then discussed the Principles for Open Scholarly Infrastructure (POSI) and how these relate to preprint servers. The POSI principles cover three elements; governance, sustainability and insurance. The POSI principles are highly relevant for preprint servers, however no server has currently adopted these.

Jennifer then presented data looking at the licenses used by preprints across different servers. Servers that allowed authors to select the preprint licenses themselves, had much greater variation in licenses used whereas servers like Research Square, which requires a CC-by license were uniform and had preprints that were much more open. Jennifer returned to the POSI commitments and invited participants to ask questions of the preprint servers as to their adherence to the POSI commitments. Jennifer ended by reinforcing that currently, biomedical preprint servers are far from these principles but that POSI represents a framework that can bring preprint servers to a much more community focussed place.

Sustainability and resources: benefits of commercial affiliation?

Following the talk by Jennifer, there was a panel discussion with representatives from Shirley Decker-lucke (SSRN), Stephanie Orphan (arXiv) and Elisa Pettinelli Barrett (Research Square). The discussion began with an overview of the three preprint servers represented and their unique features. The panel then addressed the theme of OA week directly with arXiv highlighting that they are financially independent and community focussed, ensuring that the community is prioritized. SSRN and Research Square both discussed the benefits that commercial backing can bring to the community such as additional features and “add-on” services provided on a fee basis. SSRN specifically pointed to their response to meta-research findings and community feedback as to how they prioritize feature development.

In any community-owned endeavor, sustainability is always a concern. This was one area in which both SSRN and Research Square were able to show the benefits of commercial partners in providing sustainability; SSRN in particular highlighted elements that would not be possible for them without commercial backing such as new discussions around the use of AI. However, arXiv illustrated that the association with a major university, Cornell, provided significant stability, even if this is no longer the source of financial backing. In the sustainability discussion, the servers agreed that open infrastructure was important. Research Square discussed the role that institutions could play in providing support and financially sustain preprint servers in the future.

The moderator next asked the panel about collaboration. A participant in the comments pointed out that all servers collaborate to an extent on interoperability aspects such as PIDs and licenses. Although the servers do not directly collaborate, arXiv holds regular meetings with bioRxiv/medRxiv to ensure they are coordinated and all panelists expressed interest in on-going joint discussions.

The panel Q&A ended with a question about globalization of the preprint servers. SSRN highlighted that they allow posting of preprints in any language as long as the metadata and abstract are provided in English. This is also the case for preprints submitted to arXiv. SSRN recently reissued some of their FAQs in Chinese due to an influx of preprints from China. Research Square added that the abundance of research in English forms a vicious cycle as this leads to more English language research. Arxiv also pointed out that there is a growing trend of countries desiring country-specific repositories.

One of the recurring themes in the panel discussion was the lack of a good open source infrastructure for preprint servers. Additionally, the role of ASAPbio in convening different stakeholders was highlighted as a means of improving collaboration and aligning protocols. All servers held community at the center of how they operate with SSRN providing examples of how they actively respond to community feedback. Panelists shared the benefits of commercial backing for preprint servers, particularly highlighting some of the new and improved features and, perhaps even more importantly, the sustainability in funding compared to other funding models.

Most wanted preprint server features: APIs, active community reviewing and advanced commenting features

Following the engaging panel discussion, participants were invited to take part in a whiteboard activity (featured image) whereby they were put in charge of designing a new preprint server. Participants were asked to consider how their server would be governed, how they would ensure sustainability and which features they would have on their own server. A flurry of activity followed with participants particularly focussing on features. Participants voted on some of their most desired features, with APIs, active community reviewing and advanced commenting features receiving votes. Hopefully the list of features will be useful for existing preprint servers to consider, with some of those present asking for more clarification on some of the desired features. When asked about how their desert-island preprint server would make decisions, community was at the heart of most comments. In particular, participants voted for frequent community surveys, an advisory board and accessibility. Community was also heavily featured in response to how participants would fund their servers, suggesting that the community heavily prefers non-commercial models such as library and funder memberships, grants and community donations. Ultimately, the exercise reinforced the vital role of community in how preprint servers operate.

This event highlighted the importance of ensuring that community comes above commercialisation whilst also reinforcing the benefits that can come by partnering with a commercial entity, including additional features and sustainability. If you missed the event, you can find a recording here.

Insights about the use of preprints in Japan and China: recap from the ASAPbio January Community Call

ASAPbio — Mon, 06 Feb 2023 00:00:00 +0000

Our first Community Call of 2023 hosted a discussion about the use of preprints by communities in East Asia. While there has been increasing use of preprints in the last few years, trends so far suggest that communities from different geographical regions are at different stages of adoption. An analysis of bioRxiv preprints by Abdill and colleagues highlighted that some countries publish more preprints, relative to their total number of research outputs. For example, China published over 15% of the world’s citable documents the year of the analysis, but contributed only 4% of the preprints. This suggests that there are different levels of awareness and/or perceptions about preprints among communities from that region.

To learn more about perceptions of preprints among researchers in East Asia, we were joined by representatives of two platforms that host preprints: Ritsuko Nakajima, from Jxiv and the Japan Science and Technology Agency, and Min Li from Sciencepaper Online and The Center for Science and Technology Development of the Ministry of Education, People’s Republic of China.

Ritsuko Nakajima provided an overview about the preprint server Jxiv. She noted that the platform fits in the context of Japan’s Open Science Policy, which has outlined a plan to develop infrastructure to support digital transformation in research. In addition, a report by Japan’s National Institute of Science and Technology Policy in 2020 looked at preprints related to COVID-19 and revealed that Japan ranked 13th among the countries that contributed COVID-19 preprints, suggesting there is scope for increasing the contribution of preprints from the country. Nakajima also explained that the ecosystem of journals in Japan includes a majority of journals that only publish in Japanese or that include a mix of content in English and Japanese; this represents how much research is being conducted in Japanese. These trends highlighted a need for a platform to share region-specific research in the language used by many Japanese researchers. Jxiv launched in March 2022 with a scope covering all research fields as well as manuscripts both in English and Japanese. Submissions to Jxiv undergo a screening process involving an evaluation by experts, and if the submission is approved, it is usually published within 48 hours. The server has so far published 123 preprints, and is planning further outreach among researchers to encourage the use of preprints, for example, as a way to fulfill green Open Access recommendations for publications from Japan.

Min Li presented about Sciencepaper Online, a platform launched in 2003 with the aims to broaden the academic communication channels available to researchers in China, and to facilitate the rapid sharing of research results. Sciencepaper Online provides options for the open publication of preprints and inclusion of journal articles, and in 2008 it established the Highlights of Sciencepaper Online journal. Upon submission to Sciencepaper Online, papers undergo in-house checks and if approved they appear as a free paper online. In addition, the authors can also pursue peer review of the manuscript as well as a publication certificate for preprints. Sciencepaper Online now has over 280,000 registered users and hosts more than a million and a half papers, 100,000 among those being preprints.

Following the presentations we engaged in a discussion with the two speakers. Attendees were interested in learning more about whether authors could take the reviews from Sciencepaper Online to submit their paper elsewhere, or whether once reviewed the paper on the platform would be considered published. Min Li explained that the reviews they provide are open and free access and can be recommended to other journals although in their experience the uptake of this option by authors has been very low. On the topic of reviews and reactions on papers, Ritsuko Nakajima noted that Jxiv does not currently have commenting features on papers; the server is considering this option, although they are aware that some researchers have expressed concern about the possibility of having critical comments publicly available on their preprints.

We asked both speakers for their thoughts on how to increase awareness and engagement with preprints among researchers in the region. The speakers highlighted the importance of connections with journals to reassure authors that they can have a preprint and also pursue publication at a journal. Min Li noted that Sciencepaper Online is trying to provide integration with journals, so that authors can submit their preprint from the platform to a number of journals for consideration in the future. Ritsuko Nakajima noted that they are encouraging journals in Japan to update their editorial policies to very clearly note that they accept papers posted as a preprint on Jxiv. They are also pursuing discussion with societies in different disciplines to increase awareness of preprints across their members.

We thank our two speakers for a great overview of their platforms and for sharing their insights into how preprints are used and perceived by researchers in East Asia. We look forward to engaging more with communities in the region to support awareness of preprints. Our Preprint FAQ is available in Chinese, and we welcome additional suggestions for preprint resources we could translate or develop specifically for Asian audiences.

Do you have a preprint in progress and want constructive feedback? Submit it for discussion at the ASAPbio-PREreview live-streamed preprint journal clubs

ASAPbio — Thu, 19 Jan 2023 00:00:00 +0000

Preprints provide a great avenue for researchers to get feedback on their work from the community. This type of community feedback is particularly valuable when gathered on early preprints, that is, on manuscripts that are still work-in-progress, prior to their submission for journal publication. The feedback from the community can allow authors to get a sense of what parts of the work are particularly appreciated by their peers, what can be improved in the write up of the research, and give them ideas for further experiments or lines of research.

To highlight the value of sharing early work via preprints and the benefits of community feedback, ASAPbio and PREreview are partnering to host live-streamed preprint journal clubs for early preprints (the event will follow the format of PREreview Live-streamed preprint journal clubs as described here). During the journal club, participants will discuss the preprint with a focus on highlighting the positive aspects of the work and on offering constructive suggestions for next steps for the study. After the collaborative discussion, we will post a summary of the discussion on PREreview’s platform for preprint reviews. The review will therefore receive a digital object identifier (DOI), and participants will have the option to be recognized for their contribution.

We invite authors of early preprints who would like feedback on their work to submit their work for discussion at one of these journal clubs.

Submit your preprint in progress

This is a pilot collaboration with a limited number of events planned (~6 over the course of 6 months). Your submission will be considered for this pilot according to the following criteria:

What do we mean by a preprint in progress?

By a preprint in progress or an early preprint, we refer to preprints that have not been submitted to a journal, that is, preprints that the authors are still working on and where they will be able to consider and/or incorporate the feedback prior to journal publication.

We will consider preprints in any life-science discipline, in English, Spanish or French. The preprints may be available on a preprint server or an open repository (e.g., Zenodo).

Preliminary studies are encouraged and there is no minimum length required, but the manuscript must contain a full description of the work, i.e., abstract, rationale, and methodological information.

Submit your preprint in progress to ASAPbio-PREreview live-streamed preprint journal club

If you have posted an early preprint or are planning to post one shortly, you can propose it for discussion at the journal club by completing this brief form. We hope that you or a co-author will be willing to join the journal club to discuss your work with attendees, please indicate in the form if one of the authors can attend the session.

The first journal club will take place in the second half of February, so we encourage submissions within the next two weeks but we will continue to consider proposals for future journal clubs so we invite submissions at any point in the next weeks.

Interested in participating as an attendee?

If you are interested in joining the journal club discussion as an attendee, please register your interest via this form or email us at iratxe.puebla@asapbio.org or vanessa@prereview.org, and we will contact you with further details about the first journal club session.

‘Preprints and open science’ workshop – Raising awareness about preprints in Sudan

ASAPbio — Thu, 15 Sep 2022 00:00:00 +0000

Post by Ehssan Moglad

On July 19, the Medicinal and Aromatics and Traditional Medicine Research Institute, National Center for Research, in Khartoum (Sudan), hosted a workshop about preprints and open science. The event was sponsored by ASAPbio and aimed to raise awareness around preprints among the local community of researchers, help them build skills about a productive use of preprints, and learn more about their place within open science.

The workshop was attended by around 50 attendees, which included PhD students and postgraduate researchers at the institute, university professors, and researchers in different roles. The audience also included attendees from various universities and institutes in Sudan with diverse academic backgrounds.

In this one-day workshop, three lectures were presented. The first lecture was presented by Dr Ehssan Moglad, associate professor at the institute and one of the 2022 ASAPbio Fellows. In this lecture, Dr Moglad provided an introduction to ASAPbio, as well as the organization’s mission and roadmap. The presentation also provided an overview of what preprints are, how preprints have developed since the initial experiments in the 1960s, and the increase in the use of preprints across disciplines in the last few years.

The second and third sessions in the workshop covered virtual lectures recorded over zoom and presented by Iratxe Puebla, ASAPbio’s Director of Strategic Initiatives & Community. These lectures explored the benefits of preprints for accelerating science communication, the landscape of preprint server, the value of preprints for individual researchers, and things to consider when choosing a preprint server. In her presentations, Iratxe delved deeper into different preprint-related topics and mentioned the benefits that preprints bring to individual researchers, and the workflow involved in posting to a preprint server. She rounded up the final lecture by providing “A 5-step guide to posting a preprint”.

After the lectures, a discussion session was opened to answer questions raised by attendees and to encourage them to share their experience or comments on the topic. One of the topics raised during the discussion was whether journals would reject manuscripts that had been preprinted, and what they could do if that happened.

The workshop participants were positive about the event and were pleased to have the chance to attend this first workshop in Sudan about preprint and open science. The workshop provided an opportunity to raise awareness about preprints in the region, providing researchers with information about the benefits of preprints and things to bear in mind to ensure a positive experience when posting a preprint of their own work.

ASAPbio is happy to support members of our community in raising awareness and fostering discussion about preprints. If you would like support for a local event at your institution, you can submit your application for support for the event here. Note that applicants must be ASAPbio Community members, you can join our Community for free at asapbio.org/asapbio-community.