Releasing a preprint is associated with more attention and citations for the peer-reviewed article, bioRxiv, 2019-07-14
AbstractPreprints in biology are gaining popularity, but release of a preprint still precedes only a fraction of peer-reviewed publications. We examined whether having a preprint on bioRxiv was associated with metrics of the corresponding peer-reviewed article. We assembled a dataset of 74,239 articles, 5,405 of which had a preprint, published in 39 journals. Based on log-linear regression and random-effects meta-analysis, articles with a preprint had a 51% higher Altmetric Attention Score and 37% more citations compared to articles without one. These associations were independent of several other article- and author-level variables (e.g., scientific subfield and last author publication age) and unrelated to journal-level variables such as access model and Impact Factor. This observational study can help researchers and publishers make informed decisions about how to incorporate preprints into their work.
biorxiv scientific-communication-and-education 200-500-users 2019The effect of bioRxiv preprints on citations and altmetrics, bioRxiv, 2019-06-23
1.AbstractA potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpAltmetric.com>Altmetric.com<jatsext-link> were used to compare citation and online sharing behaviour of bioRxiv preprints, their related journal articles, and non-deposited articles published in the same journals. We found that bioRxiv-deposited journal articles received a sizeable citation and altmetric advantage over non-deposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the article and its authorship. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has been subsequently published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.
biorxiv scientific-communication-and-education 200-500-users 2019Teaching R in the undergraduate ecology classroom approaches, lessons learned, and recommendations, bioRxiv, 2019-06-11
AbstractEcology requires training in data management and analysis. In this paper, we present data from the last 10 years demonstrating the increase in the use of R, an open-source programming environment, in ecology and its prevalence as a required skill in job descriptions. Because of its transparent and flexible nature, R is increasingly used for data management and analysis in the field of ecology. Consequently, job postings targeting candidates with a bachelor’s degree and a required knowledge of R have increased over the past ten years. We discuss our experiences teaching undergraduates R in two advanced ecology classes using different approaches. One approach, in a course with a field lab, focused on collecting, cleaning, and preparing data for analysis. The other approach, in a course without a field lab, focused on analyzing existing data sets and applying the results to content discussed in the lecture portion of the course. Our experiences determined that each approach had strengths and weaknesses. We recommend that above all, instructors of ecology and related subjects should be encouraged to include R in their coursework. Furthermore, instructors should be aware of the following learning R is a separate skill from learning statistics; writing R assignments is a significant time sink for course preparation; and, there is a tradeoff between teaching R and teaching content. Determining how one’s course fits into the curriculum and identifying resources outside of the classroom for students’ continued practice will ensure that R training is successful and will extend beyond a one-semester course.
biorxiv scientific-communication-and-education 0-100-users 2019The Mastery Rubric for Bioinformatics supporting design and evaluation of career-spanning education and training, bioRxiv, 2019-06-02
AbstractAs the life sciences have become more data intensive, the pressure to incorporate the requisite training into life-science education and training programs has increased. To facilitate curriculum development, various sets of (bio)informatics competencies have been articulated; however, these have proved difficult to implement in practice. Addressing this issue, we have created a curriculum-design and -evaluation tool to support the development of specific Knowledge, Skills and Abilities (KSAs) that reflect the scientific method and promote both bioinformatics practice and the achievement of competencies. Twelve KSAs were extracted via formal analysis, and stages along a developmental trajectory, from uninitiated student to independent practitioner, were identified. Demonstration of each KSA by a performer at each stage was initially described (Performance Level Descriptors, PLDs), evaluated, and revised at an international workshop. This work was subsequently extended and further refined to yield the Mastery Rubric for Bioinformatics (MR-Bi). The MR-Bi was validated by demonstrating alignment between the KSAs and competencies, and its consistency with principles of adult learning. The MR-Bi tool provides a formal framework to support curriculum building, training, and self-directed learning. It prioritizes the development of independence and scientific reasoning, and is structured to allow individuals (regardless of career stage, disciplinary background, or skill level) to locate themselves within the framework. The KSAs and their PLDs promote scientific problem formulation and problem solving, lending the MR-Bi durability and flexibility. With its explicit developmental trajectory, the tool can be used by developing or practicing scientists to direct their (and their team’s) acquisition of new, or to deepen existing, bioinformatics KSAs. The MR-Bi can thereby contribute to the cultivation of a next generation of bioinformaticians who are able to design reproducible and rigorous research, and to critically analyze results from their own, and others’, work.
biorxiv scientific-communication-and-education 200-500-users 2019Rock the Chalk A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint, bioRxiv, 2019-05-28
AbstractThe rise of electronic assisted presentation programs such as PowerPoint in undergraduate large lecture biology classes has displaced more traditional hand-drawn lectures such as the blackboard or overhead projectors, referred here as “chalk-talk” approaches. But which method is more effective in a large lecture microbiology classroom is unclear. Here I present data from a large microbial genetics lecture course taken during a five-year span comparing PowerPoint to chalk-talk lecturing methods. The results indicate that the chalk-talk approach was preferred by the students and rated higher in all measured metrics including course enjoyment, learning of key concepts, and course outcomes.
biorxiv scientific-communication-and-education 200-500-users 2019The Increasing Importance of Fellowships and Career Development Awards in the Careers of Early-Stage Biomedical Academic Researchers, bioRxiv, 2019-05-03
AbstractExcessive competition for biomedical faculty positions has ratcheted up the need to accumulate some mix of high-quality publications and prestigious grants to move from a training position to university faculty. How universities value each of these attributes when considering faculty candidates is critical for understanding what is needed to succeed as academic faculty. In this study, I analyzed publicly available NIH grant information to determine the grants first-time R01 (FTR01) awardees held during their training period. Increases in the percentage of the FTR01 population that held a training award demonstrate these awards are becoming a more common component of a faculty candidate’s resume. The increase was largely due to an expansion of NIH K-series career development awards between 2000 and 2017. FTR01 awardees with a K01, K08, K23, or K99 award were overrepresented in a subset of institutions, whereas FTR01 awardees with F32 fellowships and those with no training award were evenly distributed across institutions. Finally, training awardees from top institutions were overrepresented in the faculty of the majority of institutions, echoing data from other fields where a select few institutions supply an overwhelming majority of the faculty for the rest of the field. These data give important insight into how trainees compete for NIH funding and faculty positions and how institutions prefer those with or without training awards.
biorxiv scientific-communication-and-education 0-100-users 2019