Archives des mots-clés : transparency

Open Up – the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science

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Authors : Christina B. Reimer, Zhang Chen, Carsten Bundt, Charlotte Eben, Raquel E. London, Sirarpi Vardanian

The present paper is the mission statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab regarding Open Science. As early-career researchers (ECRs) in the lab, we first state our personal motivation to conduct research based on the principles of Open Science.

We then describe how we incorporate four specific Open Science practices (i.e., Open Methodology, Open Data, Open Source, and Open Access) into our scientific workflow. In more detail, we explain how Open Science practices are embedded into the so-called ‘co-pilot’ system in our lab.

The ‘co-pilot’ researcher is involved in all tasks of the ‘pilot’ researcher, that is designing a study, double-checking experimental and data analysis scripts, as well as writing the manuscript.

The lab has set up this co-pilot system to increase transparency, reduce potential errors that could occur during the entire workflow, and to intensify collaborations between lab members.

Finally, we discuss potential solutions for general problems that could arise when practicing Open Science.

URL : Open Up – the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science

DOI : http://doi.org/10.5334/pb.494

Survey on Scientific Shared Resource Rigor and Reproducibility

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Authors : Kevin L. Knudtson, Robert H. Carnahan, Rebecca L. Hegstad-Davies, Nancy C. Fisher, Belynda Hicks, Peter A. Lopez, Susan M. Meyn, Sheenah M. Mische, Frances Weis-Garcia, Lisa D. White, Katia Sol-Church

Shared scientific resources, also known as core facilities, support a significant portion of the research conducted at biomolecular research institutions.

The Association of Biomolecular Resource Facilities (ABRF) established the Committee on Core Rigor and Reproducibility (CCoRRe) to further its mission of integrating advanced technologies, education, and communication in the operations of shared scientific resources in support of reproducible research.

In order to first assess the needs of the scientific shared resource community, the CCoRRe solicited feedback from ABRF members via a survey. The purpose of the survey was to gain information on how U.S. National Institutes of Health (NIH) initiatives on advancing scientific rigor and reproducibility influenced current services and new technology development.

In addition, the survey aimed to identify the challenges and opportunities related to implementation of new reporting requirements and to identify new practices and resources needed to ensure rigorous research.

The results revealed a surprising unfamiliarity with the NIH guidelines. Many of the perceived challenges to the effective implementation of best practices (i.e., those designed to ensure rigor and reproducibility) were similarly noted as a challenge to effective provision of support services in a core setting. Further, most cores routinely use best practices and offer services that support rigor and reproducibility.

These services include access to well-maintained instrumentation and training on experimental design and data analysis as well as data management. Feedback from this survey will enable the ABRF to build better educational resources and share critical best-practice guidelines.

These resources will become important tools to the core community and the researchers they serve to impact rigor and transparency across the range of science and technology.

DOI : https://dx.doi.org/10.7171%2Fjbt.19-3003-001

The effect of publishing peer review reports on referee behavior in five scholarly journals

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Authors : Giangiacomo Bravo, Francisco Grimaldo, Emilia López-Iñesta, Bahar Mehmani, Flaminio Squazzoni

To increase transparency in science, some scholarly journals are publishing peer review reports. But it is unclear how this practice affects the peer review process. Here, we examine the effect of publishing peer review reports on referee behavior in five scholarly journals involved in a pilot study at Elsevier.

By considering 9,220 submissions and 18,525 reviews from 2010 to 2017, we measured changes both before and during the pilot and found that publishing reports did not significantly compromise referees’ willingness to review, recommendations, or turn-around times.

Younger and non-academic scholars were more willing to accept to review and provided more positive and objective recommendations. Male referees tended to write more constructive reports during the pilot.

Only 8.1% of referees agreed to reveal their identity in the published report. These findings suggest that open peer review does not compromise the process, at least when referees are able to protect their anonymity.

URL : The effect of publishing peer review reports on referee behavior in five scholarly journals

DOI : https://doi.org/10.1038/s41467-018-08250-2

Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

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Authors : Joshua D. Wallach, Kevin W. Boyack, John P. A. Ioannidis

Currently, there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature. According to a previous evaluation of 441 biomedical journals articles published in 2000–2014, the biomedical literature largely lacked transparency in important dimensions.

Here, we surveyed a random sample of 149 biomedical articles published between 2015 and 2017 and determined the proportion reporting sources of public and/or private funding and conflicts of interests, sharing protocols and raw data, and undergoing rigorous independent replication and reproducibility checks.

We also investigated what can be learned about reproducibility and transparency indicators from open access data provided on PubMed. The majority of the 149 studies disclosed some information regarding funding (103, 69.1% [95% confidence interval, 61.0% to 76.3%]) or conflicts of interest (97, 65.1% [56.8% to 72.6%]).

Among the 104 articles with empirical data in which protocols or data sharing would be pertinent, 19 (18.3% [11.6% to 27.3%]) discussed publicly available data; only one (1.0% [0.1% to 6.0%]) included a link to a full study protocol. Among the 97 articles in which replication in studies with different data would be pertinent, there were five replication efforts (5.2% [1.9% to 12.2%]).

Although clinical trial identification numbers and funding details were often provided on PubMed, only two of the articles without a full text article in PubMed Central that discussed publicly available data at the full text level also contained information related to data sharing on PubMed; none had a conflicts of interest statement on PubMed.

Our evaluation suggests that although there have been improvements over the last few years in certain key indicators of reproducibility and transparency, opportunities exist to improve reproducible research practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed.

URL : Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

DOI : https://doi.org/10.1371/journal.pbio.2006930

Dimensions of open research: critical reflections on openness in the ROER4D project

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Authors : Thomas William King, Cheryl-Ann Hodgkinson-Williams, Michelle Willmers, Sukaina Walji

Open Research has the potential to advance the scientific process by improving the transparency, rigour, scope and reach of research, but choosing to experiment with Open Research carries with it a set of ideological, legal, technical and operational considerations.

Researchers, especially those in resource-constrained situations, may not be aware of the complex interrelations between these different domains of open practice, the additional resources required, or how Open Research can support traditional research practices.

Using the Research on Open Educational Resources for Development (ROER4D) project as an example, this paper attempts to demonstrate the interrelation between ideological, legal, technical and operational openness; the resources that conducting Open Research requires; and the benefits of an iterative, strategic approach to one’s own Open Research practice.

In this paper we discuss the value of a critical approach towards Open Research to ensure better coherence between ‘open’ ideology (embodied in strategic intention) and ‘open’ practice (the everyday operationalisation of open principles).

URL : Dimensions of open research: critical reflections on openness in the ROER4D project

Alternative location : https://www.openpraxis.org/index.php/OpenPraxis/article/view/285

Open and transparent research practices and public perceptions of the trustworthiness of agricultural biotechnology organizations

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Authors : Asheley R. Landrum, Joseph Hilgard, Robert B. Lull, Heather Akin, Kathleen Hall Jamieson

Public trust in agricultural biotechnology organizations that produce so-called ‘genetically-modified organisms’ (GMOs) is affected by misinformed attacks on GM technology and worry that producers’ concern for profits overrides concern for the public good.

In an experiment, we found that reporting that the industry engages in open and transparent research practices increased the perceived trustworthiness of university and corporate organizations involved with GMOs.

Universities were considered more trustworthy than corporations overall, supporting prior findings in other technology domains.

The results suggest that commitment to, and communication of, open and transparent research practices should be part of the process of implementing agricultural biotechnologies.

URL : Open and transparent research practices and public perceptions of the trustworthiness of agricultural biotechnology organizations

DOI : https://doi.org/10.22323/2.17020204

Research Transparency: A Preliminary Study of Disciplinary Conceptualisation, Drivers, Tools and Support Services

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Authors : Liz Lyon, Wei Jeng, Eleanor Mattern

This paper describes a preliminary study of research transparency, which draws on the findings from four focus group sessions with faculty in chemistry, law, urban and social studies, and civil and environmental engineering.

The multi-faceted nature of transparency is highlighted by the broad ways in which the faculty conceptualised the concept (data sharing, ethics, replicability) and the vocabulary they used with common core terms identified (data, methods, full disclosure).

The associated concepts of reproducibility and trust are noted. The research lifecycle stages are used as a foundation to identify the action verbs and software tools associated with transparency.

A range of transparency drivers and motivations are listed. The role of libraries and data scientists is discussed in the context of the provision of transparency services for researchers.

URL : Research Transparency: A Preliminary Study of Disciplinary Conceptualisation, Drivers, Tools and Support Services

DOI : https://doi.org/10.2218/ijdc.v12i1.530