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Background The efforts to contain SARS-CoV-2 and reduce the impact of the COVID-19 pandemic have been supported by Test, Trace and Isolate (TTI) systems in many settings, including the United Kingdom. Mathematical models of transmission and TTI interventions, used to inform design and policy choices, make assumptions about the public’s behaviour in the context of a rapidly unfolding and changeable emergency. This study investigates public perceptions and interactions with UK TTI policy in July 2021, assesses them against how TTI processes are conceptualised and represented in models, and then interprets the findings with modellers who have been contributing evidence to TTI policy. Methods 20 members of the public recruited via social media were interviewed for one hour about their perceptions and interactions with the UK TTI system. Thematic analysis identified key themes, which were then presented back to a workshop of pandemic infectious disease modellers who assessed these findings against assumptions made in TTI intervention modelling. Workshop members co-drafted this report. Results Themes included education about SARS-CoV-2, perceived risks, trust, mental health and practical concerns. Findings covered testing practices, including the uses of and trust in different types of testing, and the challenges of testing and isolating faced by different demographic groups. This information was judged as consequential to the modelling process, from guiding the selection of research questions, influencing choice of model structure, informing parameter ranges and validating or challenging assumptions, to highlighting where model assumptions are reasonable or where their poor reflection of practice might lead to uninformative results. Conclusions We conclude that deeper engagement with members of the public should be integrated at regular stages of public health intervention modelling.

International government guidance recommends patient and public involvement (PPI) to improve the relevance and quality of research. PPI is defined as research being carried out ‘with’ or ‘by’ patients and members of the public rather than ‘to’, ‘about’ or ‘for’ them ( http://www.invo.org.uk/). Patient involvement is different from collecting data from patients as participants. Ethical considerations also differ. PPI is about patients actively contributing through discussion to decisions about research design, acceptability, relevance, conduct and governance from study conception to dissemination. Occasionally patients lead or do research. The research methods of PPI range from informal discussions to partnership research approaches such as action research, co-production and co-learning. This article discusses how researchers can involve patients when they are applying for research funding and considers some opportunities and pitfalls. It reviews research funder requirements, draws on the literature and our collective experiences as clinicians, patients, academics and members of UK funding panels.

Science communication has the potential to reshape public understanding of science. Yet, some research findings are more difficult to explain and more likely to be misunderstood. The contribution of this paper is threefold. It opens with a review of fascinating interdisciplinary literature on how scientific research about human genetics is disseminated in the media, and how this type of information could influence public beliefs and world views. It then presents the theoretical framework for my research program, providing a logical basis for how messages about human genetics may influence people's beliefs about the role of genes in causing human traits. Based on this reasoning, I formulate the genetic interpolation hypothesis, which predicts that messages about specific research findings in behavioral genetics can lead members of the public to infer greater genetic causation for other social traits not mentioned in the content of the message. While this framework offers clear, testable predictions, some questions remain unaddressed. For instance, what kind of message formats are persuasive enough to alter people's views? The third contribution of this paper is to begin to address this question empirically. I present the results of a survey experiment that was designed to test whether a simple, short paragraph about behavioral genetics is a powerful enough stimulus to cause the genetic interpolation effect.

There is a lack of datasets in Colombia that characterize the nutritional components and other similar information about food items. This study describes a structured process to develop datasets that captures the preferences and purchases of food items by a selected group of people. The datasets would classify products according to their sodium and sugar content. The outcome of this structured process would include three datasets, each with a different focus: the first contains data on food preferences, the second contains the purchase history according to the invoices obtained, and the third contains characteristics of the food items such as its brand, category, sodium and sugar content levels, among others.

Background . The major challenges that prevent the wide-scale adoption of emerging personal clean energy production are unawareness and low self-confidence. We tested a hypothesis that a combination of a new technology and educational methods could lead to the increase in awareness of children to clean energy possibilities and to an increase in self-confidence in applying them. Methods . Here we report on a toolkit that combines low carbon, clean energy source, Zn/Cu/potato batteries, sufficient to power light-emitting diodes, with a non-formal education by experience program, based on case studies and hands-on experience with battery assembly for 6-11 years old children, led by trained 12-14 old youth leaders. Results . The results show that the education experience increased the awareness of the children to produce electricity at home from unconventional, yet available raw materials and their self-confidence in being able to do this (p=0.008). Conclusions. The developed toolkit supports environmental and energy literacy education through non-formal training, increasing awareness and self-confidence in children to actually apply this in their living environment to produce clean energy.

The emergence and re-emergence of infectious diseases such as Ebola, chikungunya, and Zika increase the necessity of knowledgeable and skilled health professionals. Massive open online courses (MOOCs) arise as opportunities that allow people around the world to participate in higher education courses. A search was conducted on specialized MOOC platforms to find courses related to outbreaks, using terms included in the list of the WHO disease outbreaks from January 1st to December 31 st, 2016. We found seven courses about Ebola, two about Zika, three about the dynamics of epidemics and pandemics, and only one course about dengue, chikungunya, and malaria. Most of the courses were conducted in English. The courses on Ebola, Zika and chikungunya were released after their last outbreak. MOOCs could be used to learn about health issues of global relevance, and with the necessity of fast divulgation of knowledge and skills. Translating the courses into more languages could give these courses more traction, and allow participation of professionals in regions affected by these outbreaks.

Next generation sequencing has radically changed research in the life sciences, in both academic and corporate laboratories. The potential impact is tremendous, yet a majority of citizens have little or no understanding of the technological and ethical aspects of this widespread adoption. We designed BeerDeCoded as a pretext to discuss the societal issues related to genomic and metagenomic data with fellow citizens, while advancing scientific knowledge of the most popular beverage of all. In the spirit of citizen science, sample collection and DNA extraction were carried out with the participation of non-scientists in the community laboratory of Hackuarium, a not-for-profit organisation that supports unconventional research and promotes the public understanding of science. The dataset presented herein contains the targeted metagenomic profile of 39 bottled beers from 5 countries, based on internal transcribed spacer (ITS) sequencing of fungal species. A preliminary analysis reveals the presence of a large diversity of wild yeast species in commercial brews. With this project, we demonstrate that coupling simple laboratory procedures that can be carried out in a non-professional environment with state-of-the-art sequencing technologies and targeted metagenomic analyses, can lead to the detection and identification of the microbial content in bottled beer.

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

The emergence and re-emergence of infectious diseases such as Ebola, chikungunya, and Zika increase the necessity of knowledgeable and skilled health professionals. Massive open online courses (MOOCs) arise as opportunities that allow people around the world to participate in higher education courses. A search was conducted on specialized MOOC platforms to find courses related to outbreaks, using terms included in the list of the WHO disease outbreaks from January 1st to December 31 st, 2016. We found seven courses about Ebola, two about Zika, three about the dynamics of epidemics and pandemics, and only one course about dengue, chikungunya, and malaria. Most of the courses were conducted in English. The courses on Ebola, Zika and chikungunya were released after their last outbreak. MOOCs could be used to learn about health issues of global relevance, and with the necessity of fast divulgation of knowledge and skills. Translating the courses into more languages could give these courses more traction, and allow participation of professionals in regions affected by these outbreaks.

Next generation sequencing has radically changed research in the life sciences, in both academic and corporate laboratories. The potential impact is tremendous, yet a majority of citizens have little or no understanding of the technological and ethical aspects of this widespread adoption. We designed BeerDeCoded as a pretext to discuss the societal issues related to genomic and metagenomic data with fellow citizens, while advancing scientific knowledge of the most popular beverage of all. In the spirit of citizen science, sample collection and DNA extraction were carried out with the participation of non-scientists in the community laboratory of Hackuarium, a not-for-profit organisation that supports unconventional research and promotes the public understanding of science. The dataset presented herein contains the targeted metagenomic profile of 39 bottled beers from 5 countries, based on internal transcribed spacer (ITS) sequencing of fungal species. A preliminary analysis reveals the presence of a large diversity of wild yeast species in commercial brews. With this project, we demonstrate that coupling simple laboratory procedures that can be carried out in a non-professional environment, with state-of-the-art sequencing technologies and targeted metagenomic analyses, can lead to the detection and identification of the microbial content in bottled beer.

Background: “Open peer review” (OPR), despite being a major pillar of Open Science, has neither a standardized definition nor an agreed schema of its features and implementations. The literature reflects this, with numerous overlapping and contradictory definitions. While for some the term refers to peer review where the identities of both author and reviewer are disclosed to each other, for others it signifies systems where reviewer reports are published alongside articles. For others it signifies both of these conditions, and for yet others it describes systems where not only “invited experts” are able to comment. For still others, it includes a variety of combinations of these and other novel methods. Methods: Recognising the absence of a consensus view on what open peer review is, this article undertakes a systematic review of definitions of “open peer review” or “open review”, to create a corpus of 122 definitions. These definitions are systematically analysed to build a coherent typology of the various innovations in peer review signified by the term, and hence provide the precise technical definition currently lacking. Results: This quantifiable data yields rich information on the range and extent of differing definitions over time and by broad subject area. Quantifying definitions in this way allows us to accurately portray exactly how ambiguously the phrase “open peer review” has been used thus far, for the literature offers 22 distinct configurations of seven traits, effectively meaning that there are 22 different definitions of OPR in the literature reviewed. Conclusions: I propose a pragmatic definition of open peer review as an umbrella term for a number of overlapping ways that peer review models can be adapted in line with the aims of Open Science, including making reviewer and author identities open, publishing review reports and enabling greater participation in the peer review process.

There is an abundance of free online tools accessible to scientists and others that can be used for online networking, data sharing and measuring research impact. Despite this, few scientists know how these tools can be used or fail to take advantage of using them as an integrated pipeline to raise awareness of their research outputs. In this article, the authors describe their experiences with these tools and how they can make best use of them to make their scientific research generally more accessible, extending its reach beyond their own direct networks, and communicating their ideas to new audiences. These efforts have the potential to drive science by sparking new collaborations and interdisciplinary research projects that may lead to future publications, funding and commercial opportunities. The intent of this article is to: describe some of these freely accessible networking tools and affiliated products; demonstrate from our own experiences how they can be utilized effectively; and, inspire their adoption by new users for the benefit of science.

ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics.

In recent years, there has been an explosion in the popularity of hackathons — creative, participant-driven meetings at which software developers gather for an intensive bout of programming, often organized in teams. Hackathons have tangible and intangible outcomes, such as code, excitement, learning, networking, and so on, whose relative merits are unclear. For example, a frequent complaint is that code is abandoned when the hackathon ends, and questions like, “which outcomes are produced most reliably?” and, “how valuable are they for participants, organizers, and sponsors?” remain open. As a first step in giving “hackology” a more rigorous footing, this paper describes the NESCent hackathon model, developed over the course of a decade to serve the academic discipline of evolutionary biology, with the dual goals of augmenting the community’s shared software infrastructure, and fostering a diverse community of practice in open scientific software development. The paper presents a detailed guide to staging a NESCent-style hackathon, along with a structured information set on nine events involving 54 team projects. NESCent hackathons have produced tangible products with downstream impacts, including prototypes that were leveraged for major funding, incremental additions to production code bases, and creative drafts (designs, standards, and proofs-of-concept) that contributed to further work. The impacts of intangible outcomes could not be assessed objectively, but the subjective experience suggests that hackathons have a positive impact by (1) providing individuals with valuable experiences, networking, and training, and (2) fostering a more cohesive community of practice by enhancing awareness of challenges and best practices and by building links of familiarity between and among resources and people. Future research that recognizes the diverse outcomes of hackathons might enable evidence-based decisions about how to design hackathons for effectiveness.

Open Online Courses (OOCs) are offered by Peoples-uni at http://ooc.peoples-uni.org to complement the courses run on a separate site for academic credit at http://courses.peoples-uni.org. They provide a wide range of online learning resources beyond those usually found in credit bearing Public Health courses. They are self-paced, and students can enrol themselves at any time and utilise Open Educational Resources free of copyright restrictions. In the two years that courses have been running, 1174 students from 100 countries have registered and among the 1597 enrolments in 14 courses, 15% gained a certificate of completion. Easily accessible and appealing to a wide geographical and professional audience, OOCs have the potential to play a part in establishing global Public Health capacity building programmes.

Background: “Open peer review” (OPR), despite being a major pillar of Open Science, has neither a standardized definition nor an agreed schema of its features and implementations. The literature reflects this, with a myriad of overlapping and often contradictory definitions. While the term is used by some to refer to peer review where the identities of both author and reviewer are disclosed to each other, for others it signifies systems where reviewer reports are published alongside articles. For others it signifies both of these conditions, and for yet others it describes systems where not only “invited experts” are able to comment. For still others, it includes a variety of combinations of these and other novel methods. Methods: Recognising the absence of a consensus view on what open peer review is, this article undertakes a systematic review of definitions of “open peer review” or “open review”, to create a corpus of 122 definitions. These definitions are then systematically analysed to build a coherent typology of the many different innovations in peer review signified by the term, and hence provide the precise technical definition currently lacking. Results: This quantifiable data yields rich information on the range and extent of differing definitions over time and by broad subject area. Quantifying definitions in this way allows us to accurately portray exactly how ambiguously the phrase “open peer review” has been used thus far, for the literature offers a total of 22 distinct configurations of seven traits, effectively meaning that there are 22 different definitions of OPR in the literature. Conclusions: Based on this work, I propose a pragmatic definition of open peer review as an umbrella term for a number of overlapping ways that peer review models can be adapted in line with the ethos of Open Science, including making reviewer and author identities open, publishing review reports and enabling greater participation in the peer review process.

Despite the growth of Open Access, potentially illegally circumventing paywalls to access scholarly publications is becoming a more mainstream phenomenon. The web service Sci-Hub is amongst the biggest facilitators of this, offering free access to around 62 million publications. So far it is not well studied how and why its users are accessing publications through Sci-Hub. By utilizing the recently released corpus of Sci-Hub and comparing it to the data of ~28 million downloads done through the service, this study tries to address some of these questions. The comparative analysis shows that both the usage and complete corpus is largely made up of recently published articles, with users disproportionately favoring newer articles and 35% of downloaded articles being published after 2013. These results hint that embargo periods before publications become Open Access are frequently circumnavigated using Guerilla Open Access approaches like Sci-Hub. On a journal level, the downloads show a bias towards some scholarly disciplines, especially Chemistry, suggesting increased barriers to access for these. Comparing the use and corpus on a publisher level, it becomes clear that only 11% of publishers are highly requested in comparison to the baseline frequency, while 45% of all publishers are significantly less accessed than expected. Despite this, the oligopoly of publishers is even more remarkable on the level of content consumption, with 80% of all downloads being published through only 9 publishers. All of this suggests that Sci-Hub is used by different populations and for a number of different reasons, and that there is still a lack of access to the published scientific record. A further analysis of these openly available data resources will undoubtedly be valuable for the investigation of academic publishing.

In this article, we describe the design and implementation of an e-internship program that BioScience Project offers high school students over the summer. Project topics are in the areas of behavioral neuroscience and brain disorders. All research, teaching, and communication is done online using open access databases and webtools, a learning management system, and Google apps. Students conduct all aspects of a research project from formulating a question to collecting and analyzing the data, to presenting their results in the form of a scientific poster. Results from a pilot study involving fifteen students indicate that students are capable of successfully completing such a project, and benefit both intellectually and professionally from participating in the e-internship program.

In 2013, illegal drug use was responsible for 1.8% of years of life lost in the European Union, alcohol was responsible for 8.2% and tobacco for 18.2%, imposing economic burdens in excess of 2.5% of GDP. No single European country has optimal governance structures for reducing the harm done by nicotine, illegal drugs and alcohol, and existing ones are poorly designed, fragmented, and sometimes cause harm. Reporting the main science and policy conclusions of a transdisciplinary five-year analysis of the place of addictions in Europe, researchers from 67 scientific institutions addressed these problems by reframing an understanding of addictions. A new paradigm needs to account for evolutionary evidence which suggests that humans are biologically predisposed to seek out drugs, and that, today, individuals face availability of high drug doses, consequently increasing the risk of harm. New definitions need to acknowledge that the defining element of addictive drugs is ‘heavy use over time’, a concept that could replace the diagnostic artefact captured by the clinical term ‘substance use disorder’, thus opening the door for new substances to be considered such as sugar. Tools of quantitative risk assessment that recognize drugs as toxins could be further deployed to assess regulatory approaches to reducing harm. Re-designed governance of drugs requires embedding policy within a comprehensive societal well-being frame that encompasses a range of domains of well-being, including quality of life, material living conditions and sustainability over time; such a frame adds arguments to the inappropriateness of policies that criminalize individuals for using drugs and that continue to categorize certain drugs as illegal. A health footprint, modelled on the carbon footprint, and using quantitative measures such as years of life lost due to death or disability, could serve as the accountability tool that apportions responsibility for who and what causes drug-related harm.

Given the emergence and reemergence of viral diseases, particularly in Latin America, we would like to provide an analysis of the patterns of research and publication on Oropouche virus (OROV). We also discuss the implications of recent epidemics in certain areas of South America, and how more clinical and epidemiological information regarding OROV is urgently needed.

Background: Exchanges between scientists and nonscientists are critical to realizing the social value of basic research. These exchanges rest in part on the willingness and ability of scientists to engage effectively in science communication activities. In this paper, we discuss the perception and willingness of basic scientists in the biological and biomedical fields to engage in science outreach. Methods: The analysis is based on qualitative data collected as part of a survey on the social value of basic research and is framed by the theory of planned behavior. This is a well-established theory of human behavior that relies on the premise that a person’s intention to engage in a behavior is the single best predictor of whether that person will in fact engage in that behavior. Results: Our data show that, while bioscientists maintain a positive attitude towards science communication, their intentions are influenced by some negative feelings with regard to how nonscientists react to science communication efforts. Interactions with institutional actors, governmental bodies and the public are particularly problematic. On the other hand, interactions with clinicians and patients are framed in positive terms. Finally, some study participants raised concerns as to their ability to communicate science effectively, the availability of time and resources, and the lack of proper rewards, particularly in terms of career advancement, for those who engage in science efforts. Conclusions: Our findings suggest that bioscientists' intentions to engage in science communication efforts must be better studied to develop empirically-informed interventions to increase scientists’ participation in science outreach efforts.

Background Citations of papers are positively influenced by the journal’s impact factor (IF). For non-open access (non-OA) journals, this influence may be due to the fact that high-IF journals are more often purchased by libraries, and are therefore more often available to researchers, than low-IF journals. This positive influence has not, however, been shown specifically for papers published in open access (OA) journals, which are universally accessible, and do not need library purchase. It is therefore important to ascertain if the IF influences citations in OA journals too. Methods 203 randomized controlled trials (102 OA and 101 non-OA) published in January 2011 were included in the study. Five-year citations for papers published in OA journals were compared to those for non-OA journals. Source papers were derived from PubMed. Citations were retrieved from Web of Science, Scopus, and Google Scholar databases. The Thompson-Reuter’s IF was used. Results OA journals were found to have significantly more citations overall compared to non-OA journals (median 15.5 vs 12, p=0.039). The IF did not correlate with citations for OA journals (Spearman’s rho =0.187, p=0.60). The increase in the citations with increasing IF was minimal for OA journals (beta coefficient = 3.346, 95% CI -0.464, 7.156, p=0.084). In contrast, the IF did show moderate correlation with citations for articles published in non-OA journals (Spearman’s rho=0.514, p Conclusion It is better to publish in an OA journal for more citations. It may not be worth paying high publishing fees for higher IF journals, because there is minimal gain in terms of increased number of citations. On the other hand, if one wishes to publish in a non-OA journal, it is better to choose one with a high IF.

Given the emergence and reemergence of viral diseases, particularly in Latin America, we would like to provide an analysis of the patterns of research and publication on Oropouche virus (OROV). We also discuss the implications of recent epidemics in certain areas of South America, and how more clinical and epidemiological information regarding OROV is urgently needed.

Open Online Courses (OOCs) are offered by Peoples-uni at http://ooc.peoples-uni.org to complement the courses run on a separate site for academic credit at http://courses.peoples-uni.org. They provide a wide range of online learning resources beyond those usually found in credit bearing Public Health courses. They are self-paced, and students can enrol themselves at any time and utilise Open Educational Resources free of copyright restrictions. In the two years that courses have been running, 1174 students from 100 countries have registered and among the 1597 enrollments in 15 courses, 15% gained a certificate of completion. Easily accessible and appealing to a wide geographical and professional audience, OOCs have the potential to play a part in establishing global Public Health capacity building programmes.

In this article, we describe the design and implementation of an e-internship program that BioScience Project offers high school students over the summer. Project topics are in the areas of behavioral neuroscience and brain disorders. All research, teaching, and communication is done online using open access databases and webtools, a learning management system, and Google apps. Students conduct all aspects of a research project from formulating a question to collecting and analyzing the data, to presenting their results in the form of a scientific poster. Results from a pilot study indicate that students are capable of comprehending and successfully completing such a project, and benefit both intellectually and professionally from participating in the e-internship program.

This editorial provides a brief overview of the 12th International Society for Computational Biology (ISCB) Student Council Symposium and the 4th European Student Council Symposium held in Florida, USA and The Hague, Netherlands, respectively. Further, the role of the ISCB Student Council in promoting education and networking in the field of computational biology is also highlighted.

Communicating science to wider lay audiences is an increasingly important part of a scientist's remit, and is something that many scientists are keen to embrace. However, based on surveys carried out amongst the UK public, as well as our own experiences in developing and delivering such activities, we believe that they are not always as effective at engaging members of the general public as they could be. In this opinion article we argue that in order to achieve more effective science communication, we need more objective-driven and long-term initiatives. As well as being implemented by the scientists themselves, funding organisations can play an important role in helping to drive such initiatives, and we suggest a list of actionable items that might allow for some of these ideas to be implemented.

Next generation sequencing has radically changed research in the life sciences, in both academic and corporate laboratories. The potential impact is tremendous, yet a majority of citizens have little or no understanding of the technological and ethical aspects of this widespread adoption. We designed BeerDeCoded as a pretext to discuss the societal issues related to genomic and metagenomic data with fellow citizens, while advancing scientific knowledge of the most popular beverage of all. In the spirit of citizen science, sample collection and DNA extraction were carried out with the participation of non-scientists in the community laboratory of Hackuarium, a not-for-profit organisation that supports unconventional research and promotes the public understanding of science. The dataset presented herein contains the targeted metagenomic profile of 39 bottled beers from 5 countries, based on internal transcribed spacer (ITS) sequencing of fungal species. A preliminary analysis reveals the presence of a large diversity of wild yeast species in commercial brews. With this project, we demonstrate that coupling simple laboratory procedures that can be carried out in a non-professional environment with state-of-the-art sequencing technologies and targeted metagenomic analyses, can lead to the detection and identification of the microbial content in bottled beer.

Background: “Open peer review” (OPR), despite being a major pillar of Open Science, has neither a standardized definition nor an agreed schema of its features and implementations. The literature reflects this, with numerous overlapping and contradictory definitions. While for some the term refers to peer review where the identities of both author and reviewer are disclosed to each other, for others it signifies systems where reviewer reports are published alongside articles. For others it signifies both of these conditions, and for yet others it describes systems where not only “invited experts” are able to comment. For still others, it includes a variety of combinations of these and other novel methods. Methods: Recognising the absence of a consensus view on what open peer review is, this article undertakes a systematic review of definitions of “open peer review” or “open review”, to create a corpus of 122 definitions. These definitions are systematically analysed to build a coherent typology of the various innovations in peer review signified by the term, and hence provide the precise technical definition currently lacking. Results: This quantifiable data yields rich information on the range and extent of differing definitions over time and by broad subject area. Quantifying definitions in this way allows us to accurately portray exactly how ambiguously the phrase “open peer review” has been used thus far, for the literature offers 22 distinct configurations of seven traits, effectively meaning that there are 22 different definitions of OPR in the literature reviewed. Conclusions: I propose a pragmatic definition of open peer review as an umbrella term for a number of overlapping ways that peer review models can be adapted in line with the aims of Open Science, including making reviewer and author identities open, publishing review reports and enabling greater participation in the peer review process.

ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics.

Open Online Courses (OOCs) are offered by Peoples-uni at http://ooc.peoples-uni.org to complement the courses run on a separate site for academic credit at http://courses.peoples-uni.org. They provide a wide range of online learning resources beyond those usually found in credit bearing Public Health courses. They are self-paced, and students can enrol themselves at any time and utilise Open Educational Resources free of copyright restrictions. In the two years that courses have been running, 1174 students from 100 countries have registered and among the 1597 enrolments in 14 courses, 15% gained a certificate of completion. Easily accessible and appealing to a wide geographical and professional audience, OOCs have the potential to play a part in establishing global Public Health capacity building programmes.

Despite the growth of Open Access, potentially illegally circumventing paywalls to access scholarly publications is becoming a more mainstream phenomenon. The web service Sci-Hub is amongst the biggest facilitators of this, offering free access to around 62 million publications. So far it is not well studied how and why its users are accessing publications through Sci-Hub. By utilizing the recently released corpus of Sci-Hub and comparing it to the data of ~28 million downloads done through the service, this study tries to address some of these questions. The comparative analysis shows that both the usage and complete corpus is largely made up of recently published articles, with users disproportionately favoring newer articles and 35% of downloaded articles being published after 2013. These results hint that embargo periods before publications become Open Access are frequently circumnavigated using Guerilla Open Access approaches like Sci-Hub. On a journal level, the downloads show a bias towards some scholarly disciplines, especially Chemistry, suggesting increased barriers to access for these. Comparing the use and corpus on a publisher level, it becomes clear that only 11% of publishers are highly requested in comparison to the baseline frequency, while 45% of all publishers are significantly less accessed than expected. Despite this, the oligopoly of publishers is even more remarkable on the level of content consumption, with 80% of all downloads being published through only 9 publishers. All of this suggests that Sci-Hub is used by different populations and for a number of different reasons, and that there is still a lack of access to the published scientific record. A further analysis of these openly available data resources will undoubtedly be valuable for the investigation of academic publishing.

Background: “Open peer review” (OPR), despite being a major pillar of Open Science, has neither a standardized definition nor an agreed schema of its features and implementations. The literature reflects this, with a myriad of overlapping and often contradictory definitions. While the term is used by some to refer to peer review where the identities of both author and reviewer are disclosed to each other, for others it signifies systems where reviewer reports are published alongside articles. For others it signifies both of these conditions, and for yet others it describes systems where not only “invited experts” are able to comment. For still others, it includes a variety of combinations of these and other novel methods. Methods: Recognising the absence of a consensus view on what open peer review is, this article undertakes a systematic review of definitions of “open peer review” or “open review”, to create a corpus of 122 definitions. These definitions are then systematically analysed to build a coherent typology of the many different innovations in peer review signified by the term, and hence provide the precise technical definition currently lacking. Results: This quantifiable data yields rich information on the range and extent of differing definitions over time and by broad subject area. Quantifying definitions in this way allows us to accurately portray exactly how ambiguously the phrase “open peer review” has been used thus far, for the literature offers a total of 22 distinct configurations of seven traits, effectively meaning that there are 22 different definitions of OPR in the literature. Conclusions: Based on this work, I propose a pragmatic definition of open peer review as an umbrella term for a number of overlapping ways that peer review models can be adapted in line with the ethos of Open Science, including making reviewer and author identities open, publishing review reports and enabling greater participation in the peer review process.

Given the emergence and reemergence of viral diseases, particularly in Latin America, we would like to provide an analysis of the patterns of research and publication on Oropouche virus (OROV). We also discuss the implications of recent epidemics in certain areas of South America, and how more clinical and epidemiological information regarding OROV is urgently needed.

In this article, we describe the design and implementation of an e-internship program that BioScience Project offers high school students over the summer. Project topics are in the areas of behavioral neuroscience and brain disorders. All research, teaching, and communication is done online using open access databases and webtools, a learning management system, and Google apps. Students conduct all aspects of a research project from formulating a question to collecting and analyzing the data, to presenting their results in the form of a scientific poster. Results from a pilot study involving fifteen students indicate that students are capable of successfully completing such a project, and benefit both intellectually and professionally from participating in the e-internship program.

Introduction: R language is a powerful tool used in a wide array of research disciplines and owes a large amount of its success to its open source and adaptable nature. The popularity of R has grown rapidly over the past two decades and the number of users and packages is increasing at a near exponential rate. This rapid growth has prompted a number of formal and informal online and text resources, the volume of which is beginning to present challenges to novices learning R. Students are often first exposed to R in upper division undergraduate classes or during their graduate studies. The way R is presented likely has consequences for the fundamental understanding of the program and language itself; user comprehension of R may be better if learning the language itself followed by conducting analyses, compared to someone who is learning another subject (e.g. statistics) using R for the first time. Consequently, an understanding of the approaches to R education is critical. Methods: To establish how students are exposed to R, we used a survey to evaluate the current use in Canadian university courses, including the context in which R is presented and the types of uses of R in the classroom. Additionally, we looked at the reasons professors either do or don’t use/teach R. Results: We found that R is used in a broad range of course disciplines beyond statistics (e.g. ecology) and just over one half of Canadian universities have at least one course that uses R. Discussion and Conclusions: Developing programming-literate students is of utmost importance and our hope is that this benchmark study will influence how post-secondary educators, as well as other programmers, approach R, specifically when developing educational and supplemental content in online, text, and package-specific formats aiding in student’s comprehension of the R language.

Background: Scientific research has linked genetic predispositions to complex social behaviors and orientations. Recent empirical work in science communication suggests that the dissemination of these research findings can impact on public beliefs about the influence of genetics. The genetic interpolation hypothesis posits that exposure to this type of news causes the public to update their views about the influence of genetics on human beings and to infer greater genetic causation for other social traits that are not mentioned in the news content. The main purpose of this study is to test whether the genetic interpolation effect also emerges following exposure to a soft treatment: a short summary paragraph rather than a real news article. It also tests if specifying that a particular gene has a marginal effect succeeds at moderating the genetic interpolation effect. Finally, the study tests a counter-hypothesis: instead of resulting from belief updating, the genetic interpolation effect is triggered by the simple act of thinking about genetics shortly before reporting beliefs. Methods: In total, 2080 respondents were recruited from a pre-existing online panel and were randomly split into four experimental groups: group 1) no message; group 2) a paragraph about how genes can impact on voting behavior; group 3) the same paragraph as group 2, plus an indication that the effect of a particular gene is small; group 4) a paragraph about how genetics impact on physical traits such as eye color. Subjects were then asked to evaluate the role of genetics in causing three traits: voting at election; intelligence; and natural hair style (curly or straight). Results: The analyses reveal no evidence supporting the genetic interpolation hypothesis, the moderation hypothesis or the counter-hypothesis. Conclusion: Overall, the results suggest that exposure to a paragraph describing how genes can impact on complex social behavior is not sufficient to trigger the genetic interpolation effect.

Science outreach improves science literacy among the public and communication skills of scientists. However, despite the array of well-documented benefits, robust outreach efforts are often absent from communities which stand to benefit the most from these initiatives. Here, we introduce “Science Fiesta,” a graduate student-led outreach initiative which utilizes cultural traditions of South Texas as a vehicle to establish self-sustaining interactions between scientists and their local community. Event assessment surveys indicated that attendees found the event both fun and educational. At the same time, graduate students who organized the event and participated in outreach reported that they strengthened a variety of professional skills important for their future careers. More importantly, the event had a substantial positive impact on enthusiasm for science outreach. Both public attendees and graduate students reported that they were likely to participate in future science outreach events, even though a majority of both groups had not been previously involved in outreach efforts. Science Fiesta is a model for a highly effective graduate student-led outreach initiative that is capable of 1) improving public scientific literacy, 2) reinforcing graduate education and career development and 3) creating a culture of science engagement within local communities.

Science outreach improves science literacy among the public and communication skills of scientists. However, despite the array of well-documented benefits, robust outreach efforts are often absent from communities which stand to benefit the most from these initiatives. Here, we introduce “Science Fiesta,” a graduate student-led outreach initiative which utilizes cultural traditions of South Texas as a vehicle to establish self-sustaining interactions between scientists and their local community. Event assessment surveys indicated that attendees found the event both fun and educational. At the same time, graduate students who organized the event and participated in outreach reported that they strengthened a variety of professional skills important for their future careers. More importantly, the event had a substantial positive impact on enthusiasm for science outreach. Both public attendees and graduate students reported that they were likely to participate in future science outreach events, even though a majority of both groups had not been previously involved in outreach efforts. Science Fiesta is a model for a highly effective graduate student-led outreach initiative that is capable of 1) improving public scientific literacy, 2) reinforcing graduate education and career development and 3) creating a culture of science engagement within local communities.

The central purpose of science is to explain (Purtill, 1970). However, who is that explanation for, and how is this explanation communicated once it has been deduced? Scientific research is typically communicated via papers in journals, with an abstract presented as a summary of that explanation. However, in many instances they may be written in a manner which is non-communicatory to a lay reader (Halliday & Martin, 2003). This study begins to investigate if poetry could be used as an alternative form of communication, by first assessing if poetic verse is an effective form of communication to other scientists. In order to assess this suitability, a survey was conducted in which two different groups of participants were asked questions based on a scientific abstract. One group of participants was given the original scientific abstract, whilst the second group was instead given a poem written about the scientific study. Quantitative analysis found that whilst a scientific audience found a poetic interpretation of a scientific abstract to be no less interesting or inspiring than the original prose, they did find it to be less accessible. However, further qualitative analysis suggested that the poem did a good job in conveying a similar meaning to that presented in the original abstract. The results of this study indicate that whilst for a scientific audience poetry should not replace the prose abstract, it could be used alongside the original format to inspire the reader to find out more about the topic. Further research is needed to investigate the effectiveness of this approach for a non-expert audience. Alternative version: Are scientific papers understood, By anyone from outside of the field; And is an abstract really any good, If jargon means its secrets aren’t revealed? Could poetry present a different way, Of summing up research in a nutshell; Presented in a language for the lay, Yet still useful for scientists as well? This study aimed to find if it was true, That poems could be a way to convey fact; By splitting sample researchers in two: And giving each a different abstract. The findings showed that whilst prose was preferred, Related meanings from both were inferred.

The first woman to earn a Professorship at a University in Europe was Laura Maria Caterina Bassi, who earned a professorship in physics at the University of Bologna in 1732. Almost 300 years and three waves of feminism later, in 2016, women typically still only comprise 20% (or less) of the number of full professors in Europe. This opinion article will discuss the experiences of being a female academic today and the factors contributing to the academic gender gap from the perspective of a “young” natural scientist, as well as providing constructive suggestions for strategies to empower women in the academic world.

The biomedical research enterprise faces considerable structural challenges after years of stagnant funding coupled with steady growth of the pool of graduate students and postdoctoral scientists. Input from junior scientists into the nature of how these challenges affect both the quality of the enterprise and career outcomes is essential to craft effective reforms that will bring a new era of robustness into biomedical research. In October 2015, junior scientists based in Chicago organized the Future of Research Chicago Symposium. The goals of the meeting were twofold: first, to educate the local community about structural problems in biomedical science; and second, to survey scientists in the Midwest, particularly postdocs, in order to find out their views on these issues and solicit suggestions for improvement. We present the recommendations of Symposium participants as distilled by the organizers. These recommendations reflect junior scientists’ desire for diversification of career development opportunities within the framework of doctoral and postdoctoral training and for policies at funding agencies that demonstrate a stronger commitment to supporting trainees and new investigators. We discuss practical steps that can be taken to enable these reforms, highlighting the responsibilities of junior scientists, faculty, funding agencies, and other stakeholders in working toward the goal of a revitalized biomedical research system.

Communicating science to wider lay audiences is of increasing importance and is becoming an ever larger part of a scientist's remit which also offers important opportunities. We discuss here the current state of science communication in the field of the natural sciences in the UK, and the enormous improvements that could be achieved through putting more weight on objective-driven long-term initiatives, ideally in the form of interdisciplinary networks, to achieve higher impact. We describe the barriers that stand in the way of such developments and make a number of suggestions how funding organisations in particular could play a major role in overcoming these barriers.

The Royal Society of Chemistry held, to our knowledge, the world’s first Twitter conference at 9am on February 5 th, 2015. The conference was a Twitter-only conference, allowing researchers to upload academic posters as tweets, replacing a physical meeting. This paper reports the details of the event and discusses the outcomes, such as the potential for the use of social media to enhance scientific communication at conferences. In particular, the present work argues that social media outlets such as Twitter broaden audiences, speed up communication, and force clearer and more concise descriptions of a researcher’s work. The benefits of poster presentations are also discussed in terms of potential knowledge exchange and networking. This paper serves as a proof-of-concept approach for improving both the public opinion of the poster, and the enhancement of the poster through an innovative online format that some may feel more comfortable with, compared to face-to-face communication.

The overall aim of public academic science communication is to engage a non-scientist with a particular field of science and/or research topic, often driven by the expertise of the academic. An e-survey was designed to provide insight into respondent’s current and future engagement with science communication activities. Respondents provided a wide range of ideas and concerns as to the ‘common practice’ of academic science communication, and whilst they support some of these popular approaches (such as open-door events and science festivals), there are alternatives that may enable wider engagement. Suggestions of internet-based approaches and digital media were strongly encouraged, and although respondents found merits in methods such as science festivals, limitations such as geography, time and topic of interest were a barrier to engagement for some. Academics and scientists need to think carefully about how they plan their science communication activities and carry out evaluations, including considering the point of view of the public, as although defaulting to hands-on open door events at their university may seem like the expected standard, it may not be the best way to reach the intended audience.

The first woman to earn a Professorship at a University in Europe was Laura Maria Caterina Bassi, who earned a professorship in physics at the University of Bologna in 1732. Almost 300 years and three waves of feminism later, in 2016, women typically still only comprise 20% (or less) of the number of full professors in Europe. This opinion article will discuss the experiences of being a female academic today and the factors contributing to the academic gender gap from the perspective of a “young” natural scientist, as well as providing constructive suggestions for strategies to empower women in the academic world.

The central purpose of science is to explain. However, who is that explanation for, and how is this explanation communicated once it has been deduced? Scientific research is typically communicated via papers in journals, with an abstract presented as a summary of that explanation. However, in many instances they may be written in a manner which is non-communicatory to a lay reader. This study begins to investigate if poetry could be used as an alternative form of communication, by first assessing if poetic verse is an effective form of communication to other scientists. In order to assess this suitability, a survey was conducted in which two different groups of participants were asked questions based on a scientific abstract. One group of participants was given the original scientific abstract, whilst the second group was instead given a poem written about the scientific study. Quantitative analysis found that whilst a scientific audience found a poetic interpretation of a scientific abstract to be no less interesting or inspiring than the original prose, they did find it to be less accessible. However, further qualitative analysis suggested that the poem did a good job in conveying a similar meaning to that presented in the original abstract. The results of this study indicate that whilst for a scientific audience poetry should not replace the prose abstract, it could be used alongside the original format to inspire the reader to find out more about the topic. Further research is needed to investigate the effectiveness of this approach for a general audience.

Many new websites and online tools have come into existence to support scholarly communication in all phases of the research workflow. To what extent researchers are using these and more traditional tools has been largely unknown. This 2015-2016 survey aimed to fill that gap. Its results may help decision making by stakeholders supporting researchers and may also help researchers wishing to reflect on their own online workflows. In addition, information on tools usage can inform studies of changing research workflows. The online survey employed an open, non-probability sample. A largely self-selected group of 20663 researchers, librarians, editors, publishers and other groups involved in research took the survey, which was available in seven languages. The survey was open from May 10, 2015 to February 10, 2016. It captured information on tool usage for 17 research activities, stance towards open access and open science, and expectations of the most important development in scholarly communication. Respondents’ demographics included research roles, country of affiliation, research discipline and year of first publication.

The central purpose of science is to explain. However, who is that explanation for, and how is this explanation communicated once it has been deduced? Scientific research is typically communicated via papers in journals, with an abstract presented as a summary of that explanation. However, in many instances they may be written in a manner which is non-communicatory to a lay reader. This study begins to investigate if poetry could be used as an alternative form of communication, by first assessing if poetic verse is an effective form of communication to other scientists. In order to assess this suitability, a survey was conducted in which two different groups of participants were asked questions based on a scientific abstract. One group of participants was given the original scientific abstract, whilst the second group was instead given a poem written about the scientific study. Quantitative analysis found that whilst a scientific audience found a poetic interpretation of a scientific abstract to be no less interesting or inspiring than the original prose, they did find it to be less accessible. However, further qualitative analysis suggested that the poem did a good job in conveying a similar meaning to that presented in the original abstract. The results of this study indicate that whilst for a scientific audience poetry should not replace the prose abstract, it could be used alongside the original format to inspire the reader to find out more about the topic. Further research is needed to investigate the effectiveness of this approach for a general audience.

The Royal Society of Chemistry held, to our knowledge, the world’s first Twitter conference at 9am on February 5 th, 2015. The conference was a Twitter-only conference, allowing researchers to upload academic posters as tweets, replacing a physical meeting. This paper reports the details of the event and discusses the outcomes, such as the potential for the use of social media to enhance scientific communication at conferences. In particular, the present work argues that social media outlets such as Twitter broaden audiences, speed up communication, and force clearer and more concise descriptions of a researcher’s work. The benefits of poster presentations are also discussed in terms of potential knowledge exchange and networking. This paper serves as a proof-of-concept approach for improving both the public opinion of the poster, and the enhancement of the poster through an innovative online format that some may feel more comfortable with, compared to face-to-face communication.