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Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

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Authors : Hannes Juergens, Matthijs Niemeijer, Laura D. Jennings-Antipov, Robert Mans, Jack More, Antonius J. A. van Maris, Jack T. Pronk, Timothy S. Gardner

Open data in science requires precise definition of experimental procedures used in data generation, but traditional practices for sharing protocols and data cannot provide the required data contextualization.

Here, we explore implementation, in an academic research setting, of a novel cloud-based software system designed to address this challenge. The software supports systematic definition of experimental procedures as visual processes, acquisition and analysis of primary data, and linking of data and procedures in machine-computable form.

The software was tested on a set of quantitative microbial-physiology experiments. Though time-intensive, definition of experimental procedures in the software enabled much more precise, unambiguous definitions of experiments than conventional protocols.

Once defined, processes were easily reusable and composable into more complex experimental flows. Automatic coupling of process definitions to experimental data enables immediate identification of correlations between procedural details, intended and unintended experimental perturbations, and experimental outcomes.

Software-based experiment descriptions could ultimately replace terse and ambiguous ‘Materials and Methods’ sections in scientific journals, thus promoting reproducibility and reusability of published studies.

URL : Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics

DOI : https://doi.org/10.1038/sdata.2018.195

Measuring Open Access Policy Compliance: Results of a Survey

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Authors : Shannon Kipphut-Smith, Michael Boock, Kimberly Chapman, Michaela Willi Hooper

INTRODUCTION

In the last decade, a significant number of institutions have adopted open access (OA) policies. Many of those working with OA policies are tasked with measuring policy compliance.

This article reports on a survey of Coalition of Open Access Policy Institutions (COAPI) members designed to better understand the methods currently used for measuring and communicating OA policy success.

METHODS

This electronic survey was distributed to the COAPI member listserv, inviting both institutions who have passed an implemented policies and those who are still developing policies to participate.

RESULTS

The results to a number of questions related to topics such as policy workflows, quantitative and qualitative measurement activities and related tools, and challenges showed a wide range of responses, which are shared here.

DISCUSSION

It is clear that a number of COAPI members struggle with identifying what should be measured and what tools and methods are appropriate. The survey illustrates how each institution measures compliance differently, making it difficult to benchmark against peer institutions.

CONCLUSION

As a result of this survey, we recommend that institutions working with OA policies be as transparent as possible about their data sources and methods when calculating deposit rates and other quantitative measures.

It is hoped that this transparency will result in the development of a set of qualitative and quantitative best practices for assessing OA policies that standardizes assessment terminology and articulates why institutions may want to measure policies.

URL : Measuring Open Access Policy Compliance: Results of a Survey

DOI : https://doi.org/10.7710/2162-3309.2247

Is It Such a Big Deal? On the Cost of Journal Use in the Digital Era

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Authors : Fei Shu, Philippe Mongeon, Stefanie Haustein, Kyle Siler, Juan Pablo Alperin, Vincent Larivière

Commercial scholarly publishers promote and sell bundles of journals—known as big deals—that provide access to entire collections rather than individual journals. Following this new model, size of serial collections in academic libraries increased almost fivefold from 1986 to 2011.

Using data on library subscriptions and references made for a sample of North American universities, this study provides evidence that, while big deal bundles do decrease the mean price per subscribed journal, academic libraries receive less value for their investment.

We find that university researchers cite only a fraction of journals purchased by their libraries, that this fraction is decreasing, and that the cost per cited journal has increased.

These findings reveal how academic publishers use product differentiation and price strategies to increase sales and profits in the digital era, often at the expense of university and scientific stakeholders.

URL : Is It Such a Big Deal? On the Cost of Journal Use in the Digital Era

DOI : https://doi.org/10.5860/crl.79.6.785

Gender and international diversity improves equity in peer review

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Authors : Dakota Murray, Kyle Siler, Vincent Lariviére, Wei Mun Chan, Andrew M. Collings, Jennifer Raymond, Cassidy R Sugimoto

The robustness of scholarly peer review has been challenged by evidence of disparities in publication outcomes based on author’s gender and nationality. To address this, we examine the peer review outcomes of 23,873 initial submissions and 7,192 full submissions that were submitted to the biosciences journal eLife between 2012 and 2017.

Women and authors from nations outside of North America and Europe were underrepresented both as gatekeepers (editors and peer reviewers) and last authors. We found a homophilic interaction between the demographics of the gatekeepers and authors in determining the outcome of peer review; that is, gatekeepers favor manuscripts from authors of the same gender and from the same country.

The acceptance rate for manuscripts with male last authors was significantly higher than for female last authors, and this gender inequity was greatest when the team of reviewers was all male; mixed-gender gatekeeper teams lead to more equitable peer review outcomes.

Similarly, manuscripts were more likely to be accepted when reviewed by at least one gatekeeper with the same national affiliation as the corresponding author. Our results indicated that homogeneity between author and gatekeeper gender and nationality is associated with the outcomes of scientific peer review.

We conclude with a discussion of mechanisms that could contribute to this effect, directions for future research, and policy implications. Code and anonymized data have been made available at https://github.com/murrayds/elife-analysis

URL : Gender and international diversity improves equity in peer review

DOI : https://doi.org/10.1101/400515

Plurality in multi-disciplinary research: multiple institutional affiliations are associated with increased citations

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Authors : Paul Sanfilippo​, Alex W. Hewitt, David A. Mackey

Background

The institutional affiliations and associated collaborative networks that scientists foster during their research careers are salient in the production of high-quality science. The phenomenon of multiple institutional affiliations and its relationship to research output remains relatively unexplored in the literature.

Methods

We examined 27,612 scientific articles, modelling the normalized citation counts received against the number of authors and affiliations held.

Results

In agreement with previous research, we found that teamwork is an important factor in high impact papers, with average citations received increasing concordant with the number of co-authors listed.

For articles with more than five co-authors, we noted an increase in average citations received when authors with more than one institutional affiliation contributed to the research.

Discussion

Multiple author affiliations may play a positive role in the production of high-impact science. This increased researcher mobility should be viewed by institutional boards as meritorious in the pursuit of scientific discovery.

URL : Plurality in multi-disciplinary research: multiple institutional affiliations are associated with increased citations

DOI : https://doi.org/10.7717/peerj.5664

Why digital natives need books: The myth of the digital native

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Author : Hildegunn Støle

This article is concerned with children’s reading development in the important years from when they begin learning to read to the age when the child reaches adequate reading comprehension to read to learn from a variety of texts on diverse subjects. Like any skill, reading skill requires relevant and extensive training.

We have tended to think that children growing up in the digital era get plenty reading training from digital devices and that this is as efficient as reading books was for earlier generations.

Due to this optimism, we have paid too little attention to whether extensive use of digital devices actually provide children with relevant reading training during the important years that efficient reading is developed. The author holds that book reading still has its place in education.

URL : http://firstmonday.org/ojs/index.php/fm/article/view/9422

Reading in a post-textual era

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Authors : Miha Kovač, Adriaan van der Weel

This paper analyses major social shifts in reading by comparing publishing statistics with results of empirical research on reading. As media statistics suggest, the last five decades have seen two shifts: from textual to visual media, and with the advent of digital screens also from long-form to short-form texts.

This was accompanied by new media-adequate reading modes: while long-form content invokes immersed and/or deep reading, we predominantly skim online social media. Empirical research on reading indicates that the reading substrate plays an important role in reading processes.

For example, comprehension suffers when complex texts are read from screens. This paper argues that media and reading trends in recent decades indicate broader social and cultural changes in which long-form deep reading traditionally associated with the printed book will be marginalised by prevailing media trends and the reading modes they inspire. As these trends persist, it may be necessary to find new approaches to vocabulary and knowledge building.

URL : http://firstmonday.org/ojs/index.php/fm/article/view/9416