genomeRxiv: a microbial whole-genome database for classification, identification, and data sharing

“genomeRxiv is a newly-funded US-UK collaboration to provide a public, web-accessible database of public genome sequences, accurately catalogued and classified by whole-genome similarity independent of their taxonomic affiliation. Our goal is to supply the basic and applied research community with rapid, precise and accurate identification of unknown isolates based on genome sequence alone, and with molecular tools for environmental analysis….”

P112?SMILE: Sustaining Medical Education In a Lockdown Environment.Using social media to develop a free online access medical education platform during lockdown | BJS Open | Oxford Academic

Abstract Introduction

SMILE is a free online access medical education (FOAMEd) platform created by two UK surgical trainees and a medical student that delivered over 200 medical lectures during lockdown.


The role of Social Media in the development of SMILE was interrogated using a survey sent to all SMILE participants and by analysing activity on SMILE social media platforms.


1306 students responded to the online survey with 57.2% saying they heard of SMILE through Facebook. Engagement using facebook remained highest with 13,819 members, over 800 user comments and >16,000 user reactions.

4% of the students heard of SMILE through Twitter or Instagram.

Facebook analytics revealed the highest level of traffic when lectures were most commonly held suggesting students used Facebook to access lectures.

Other educators were able to find SMILE on social media, leading to collaborations with other platforms.

Throughout the survey many mentioned how social media created and maintained a community of medical students enhancing group-based learning


We demonstrate that social media platforms provide popular and cost-effective methods to promote, sustain & deliver medical education for students and educators.

COVID-19 and the research scholarship ecosystem: help! – Journal of Clinical Epidemiology


Data sharing is not common as part of biomedical publications
To increase data sharing biomedical journals, funders and academic institutions should introduce policies that will enhance data sharing and other open science practices
As part of research assessments incentives and rewards need to be introduced



Data sharing practices remain elusive in biomedicine. The COVID-19 pandemic has highlighted the problems associated with the lack of data sharing. The objective of this article is to draw attention to the problem and possible ways to address it.

Study Design and Setting

This article examines some of the current open access and data sharing practices at biomedical journals and funders. In the context of COVID-19 the consequences of these practices is also examined.


Despite the best of intentions on the part of funders and journals, COVID-19 biomedical research is not open. Academic institutions need to incentivize and reward data sharing practices as part of researcher assessment. Journals and funders need to implement strong polices to ensure that data sharing becomes a reality. Patients support sharing of their data.


Biomedical journals, funders and academic institutions should act to require stronger adherence to data sharing policies.

Awareness of predatory journals and open access publishing among orthopaedic and trauma surgeons – results from an online survey in Germany | BMC Musculoskeletal Disorders | Full Text

Abstract:  Background

Along with emerging open access journals (OAJ) predatory journals increasingly appear. As they harm accurate and good scientific research, we aimed to examine the awareness of predatory journals and open access publishing among orthopaedic and trauma surgeons.


In an online survey between August and December 2019 the knowledge on predatory journals and OAJ was tested with a hyperlink made available to the participants via the German Society for Orthopaedics and Trauma Surgery (DGOU) email distributor.


Three hundred fifty orthopaedic and trauma surgeons participated, of which 291 complete responses (231 males (79.4%), 54 females (18.6%) and 5?N/A (2.0%)) were obtained. 39.9% were aware of predatory journals. However, 21.0% knew about the “Directory of Open Access Journals” (DOAJ) as a register for non-predatory open access journals. The level of profession (e.g. clinic director, consultant) (p =?0.018) influenced the awareness of predatory journals. Interestingly, participants aware of predatory journals had more often been listed as corresponding authors (p <?0.001) and were well published as first or last author (p <?0.001). Awareness of OAJ was masked when journal selection options did not to provide any information on the editorial board, the peer review process or the publication costs.


The impending hazard of predatory journals is unknown to many orthopaedic and trauma surgeons. Early stage clinical researchers must be trained to differentiate between predatory and scientifically accurate journals.

Characterization of an open access medical news platform readership during the COVID-19 pandemic

Abstract:  Background:

There now exists many alternatives to direct journal access, such as podcasts, blogs, and news sites for physicians and the general public to stay up-to-date with medical literature. Currently however, there is a scarcity of literature that investigates these readership characteristics of open access medical news sites and how they may have shifted with coronavirus disease 19 (COVID-19).


The current study aimed to employ readership and survey data to characterize open access medical news readership trends in relation to COVID-19 in addition to overall readership trends regarding pandemic related information delivery.


Anonymous aggregate readership data was obtained from 2 Minute Medicine® (, an open-access, physician-run medical news organization that has published over 8000 original physician-written text and visual summaries of new medical research since 2013. In this retrospective observational study, the average article views, actions (defined as the sum of views, shares, and outbound link clicks), read times, and bounce rate (probability to leave a page in <30s) were compared between COVID-19 articles published between January 1 to May 31, 2020 (N = 40) to non-COVID-19 articles (N = 145) published in the same time period. A voluntary survey was also sent to subscribed 2 Minute Medicine readers to further characterize readership demographics and preferences scored by Likert Scale.


COVID-19 articles had significantly more median views than non-COVID-19 articles (296 vs. 110, U = 748.5, P < 0.001). There were no differences in average read times or bounce rate. Non-COVID-19 had more median actions than COVID-19 articles (2.9 vs. 2.5, U = 2070.5, P < 0.05). On a Likert scale of 1 (Strongly Disagree) to 5 (Strongly Agree), survey data revealed that 66% (78/119) of readers Agreed or Strongly Agreed that they preferred staying up to date with emerging literature surrounding COVID-19 using sources such as 2 Minute Medicine versus direct journal access. A greater proportion of survey takers also indicated open access news sources to be one of their primary means of staying informed (71.7%) than direct journal article access (50.8%). A lesser proportion of readers indicated reading one or less full length medical study following introduction to 2 Minute Medicine compared to prior (16.9% vs. 31.8%, P < 0.05).


There is a significantly increased readership in one open-access medical literature platform during the pandemic, reinforcing that open-access physician-written sources of medical news represent an important alternative to direct journal access for readers to stay up to date with medical literature.

Actives from MMV Open Access Boxes? A suggested way forward

Abstract:  It is estimated that more than 1 billion people across the world are affected by a neglected tropical disease (NTD) that requires medical intervention. These diseases tend to afflict people in areas with high rates of poverty and cost economies billions of dollars every year. Collaborative drug discovery efforts are required to reduce the burden of these diseases in endemic regions. The release of “Open Access Boxes” is an initiative launched by Medicines for Malaria Venture (MMV) in collaboration with its partners to catalyze new drug discovery in neglected diseases. These boxes are mainly requested by biology researchers across the globe who may not otherwise have access to compounds to screen nor knowledge of the workflow that needs to be followed after identification of actives from their screening campaigns. Here, we present guidelines on how to move such actives beyond the hit identification stage, to help in capacity strengthening and enable a greater impact of the initiative.



Open Science and the emergence of preprints

“In the context of this journal, Revista Gaúcha de Enfermagem, the debate on the particularities regarding the new preprint model of publication has been a present topic and has stimulated intense debate in the scientific communication and editorial communities considering the contradictions that surround this model. At the same time, the editors have been consulted regarding the priority action lines of SciELO, the Scientific Electronic Library Online, in order to consolidate their own preprint repository, according to the international scientific publication trends towards Open Science, which has been integrating more and more the debate in forums and specific events (1-2….”

Broader reach in searching for adverse events articles – a case study with DOAJ and Crossref

“An efficient strategy for searching for adverse events in scientific literature should find as many relevant events as possible and maintain screening effort within reasonable levels.


Naturally, finding more adverse events is directly related to the question of where to search. Past studies suggest results do improve when searching multiple established proprietary global literature databases. We decided to investigate databases that favor open models of scholarly publications, now gaining traction in the academic world. Can they be a cost-effective way to more adverse events results from the literature?


In this post, we investigate the use of alternative scientific literature sources to complement searching for adverse events on a mainstream index (PubMed). In particular we explored:

The Directory of Open Access Journals (DOAJ) indexes academic literature with an open access license from publishers worldwide. It currently hosts over 5 million records.

Crossref: a community organization dedicated to supporting scholarly communication by generating metadata and providing services for content discoverability. The Crossref metadata spans over 120 million records, with a growing proportion being published as open abstracts….”