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A guideline for reporting experimental protocols in life sciences

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Authors : Olga Giraldo​, Alexander Garcia, Oscar Corcho

Experimental protocols are key when planning, performing and publishing research in many disciplines, especially in relation to the reporting of materials and methods. However, they vary in their content, structure and associated data elements.

This article presents a guideline for describing key content for reporting experimental protocols in the domain of life sciences, together with the methodology followed in order to develop such guideline.

As part of our work, we propose a checklist that contains 17 data elements that we consider fundamental to facilitate the execution of the protocol. These data elements are formally described in the SMART Protocols ontology.

By providing guidance for the key content to be reported, we aim (1) to make it easier for authors to report experimental protocols with necessary and sufficient information that allow others to reproduce an experiment, (2) to promote consistency across laboratories by delivering an adaptable set of data elements, and (3) to make it easier for reviewers and editors to measure the quality of submitted manuscripts against an established criteria.

Our checklist focuses on the content, what should be included. Rather than advocating a specific format for protocols in life sciences, the checklist includes a full description of the key data elements that facilitate the execution of the protocol.

URL : A guideline for reporting experimental protocols in life sciences

DOI : https://doi.org/10.7717/peerj.4795

Leveraging Elsevier’s Creative Commons License Requirement to Undermine Embargo

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Author : Josh Bolick

In the last round of author-sharing policy revisions, Elsevier created a labyrinthine title-by-title embargo structure requiring embargoes from 12 to 48 months for authors sharing via institutional repository (IR), while permitting immediate sharing via an author’s personal website or blog. At the same time, all prepublication versions are to bear a Creative Commons-Attribution-Noncommercial-No Derivatives (CC-BY-NC-ND) license.

At the time this policy was announced, it was criticized by many in the scholarly communication community as overly complicated and restrictive. However, this CC licensing requirement creates an avenue for subverting an embargo in the IR to achieve quicker and wider open distribution of the author’s accepted manuscript (AAM).

To wit, authors may post an appropriately licensed copy on their personal site or blog, at which point the author’s host institution may deposit without an embargo in the IR, not through the license granted in the publication agreement, but through the CC license on the author’s version, which the sharing policy mandates.

This article outlines the background and rationale of the issue and discusses the benefits, workflows, and remaining questions.

URL : Leveraging Elsevier’s Creative Commons License Requirement to Undermine Embargo

DOI : https://doi.org/10.17161/jcel.v2i2.7415

Towards a Decentralized Process for Scientific Publication and Peer Review using Blockchain and IPFS

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Authors : Antonio Tenorio-Fornés, Viktor Jacynycz, David Llop, Antonio A. Sanchez-Ruiz, Samer Hassan

The current processes of scientific publication and peer review raise concerns around fairness, quality, performance, cost, and accuracy. The Open Access movement has been unable to fulfill all its promises, and a few middlemen publishers can still impose policies and concentrate profits.

This paper, using emerging distributed technologies such as Blockchain and IPFS, proposes a decentralized publication system for open science.

The proposed system would provide (1) a distributed reviewer reputation system, (2) an Open Access by-design infrastructure, and (3) transparent governance processes.

A survey is used to evaluate the problems, proposed solutions and possible adoption resistances, while a working prototype serves as a proof-of-concept.

Additionally, the paper discusses the implementation, in a distributed context, of different privacy settings for both open peer review and reputation systems, introducing a novel approach supporting both anonymous and accountable reviews. The paper concludes reviewing the open challenges of this ambitious proposal.

URL : Towards a Decentralized Process for Scientific Publication and Peer Review using Blockchain and IPFS

The use and perceptions of open Access resources by legal academics at the University of Cape Town (UCT) in South Africa

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Author : Elizabeth Moll-Willard

Although access to primary legal materials in South Africa is now easily accessible as a result of the Free Access to Law movement, access to legal scholarship is not as easy.

Through using the University of Cape Town (UCT) as a case study, due to its research intensive nature, it is possible to see how academics are publishing their legal scholarship through the use of bibliometrics and data mining.

After the success of a Research Visibility month, law librarians were able to attest to the perceptions of legal academics around the importance of the openness and visibility of their research.

The author contrasts these two to see if the perception of legal academics around the visibility of their resources reflects their publishing practices. It is seen that although academics at UCT publish mostly in closed journals, the publishing in open and hybrid journals has slowly increased during the period 2011-2015.

Further it is evidenced that legal academics are exploring other avenues, including that of self-archiving, to boost the visibility of their work. Law Librarians are able to assist in boosting at least the visibility, if not the openness of legal academics’ work.

URL : The use and perceptions of open Access resources by legal academics at the University of Cape Town (UCT) in South Africa

Alternative location : https://ojs.law.cornell.edu/index.php/joal/article/view/78

How significant are the public dimensions of faculty work in review, promotion, and tenure documents?

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Authors : Juan Pablo Alperin, Gustavo E. Fischman, Erin C. McKiernan, Carol Muñoz Nieves, Meredith T. Niles, Lesley Schimanski

Much of the work of universities, even private institutions, has significant public dimensions. Faculty work in particular is often funded by public funds, is aimed at serving the public good, and is subject to public evaluation.

To understand how the public dimensions of faculty work are valued, we analyzed review, tenure and promotion documents from a representative sample of 129 Canadian and American universities.

We found terms and concepts related to public and community are mentioned in a large portion of documents, but mostly in ways that relate to service—an undervalued aspect of academic careers.

Moreover, we find significant mentions of traditional research outputs and citation-based metrics. Such outputs and metrics reward faculty work targeted to academics, and mostly disregard the public dimensions.

We conclude that institutions that want to live up to their public mission need to work towards systemic change in how faculty work is assessed and incentivized.

URL : How significant are the public dimensions of faculty work in review, promotion, and tenure documents?

DOI : https://hcommons.org/deposits/item/hc:21015

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