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Analytical code sharing practices in biomedical research

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Authors : Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande et al.

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared.

We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10−9).

Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10−07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research.

By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

URL : Analytical code sharing practices in biomedical research

DOI : https://doi.org/10.1101/2023.07.31.551384

The Effects of Research Data Management Services: Associating the Data Curation Lifecycle with Open Research Output

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Authors : Nicolas Pares, Peter Organisciak

This study seeks to understand the relationship between research data management (RDM) services framed in the data curation life cycle and the production of open data. An electronic questionnaire was distributed to US researchers and RDM specialists, and the results were analyzed using Chi-Square tests for association.

The data curation life cycle does associate with the production of open data and shareable research, but tasks like data management plans have stronger associations with the production of open data. The findings analyze the intersection of these concepts and provide insight into RDM services that facilitate the production of open data and shareable research.

URL : The Effects of Research Data Management Services: Associating the Data Curation Lifecycle with Open Research Output

DOI : https://doi.org/10.5860/crl.84.5.751

Viewing research assessment, the academic reward system, and academic publishing through the power/knowledge lens of Foucault

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Author : Timothy D. Bowman

The academic research assessment system, the academic reward system, and the academic publishing system are interrelated mechanisms that facilitate the scholarly production of knowledge.

This article considers these systems using a Foucauldian lens to examine the power/knowledge relationships found within and through these systems. A brief description of the various systems is introduced followed by examples of instances where Foucault’s power, knowledge, discourse, and power/knowledge concepts are useful to provide a broader understanding of the norms and rules associated with each system, how these systems form a network of power relationships that reinforce and shape one another.

URL : Viewing research assessment, the academic reward system, and academic publishing through the power/knowledge lens of Foucault

DOI : https://doi.org/10.3389/frma.2023.1179376

Simulating and Contrasting the Game of Open Access in Diverse Cultural Contexts: A Social Simulation Model

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Authors : Oswaldo Terán, Jacinto Dávila

Open Access is a global cause with the aim of allowing unrestricted access to all scientific research output in electronic formats. This paper presents a model for simulating the game of interests behind this cause in order to investigate ways of promoting the practice of open access. The model represents the following actors: Academics, Administrators, Funders, Publishers and Politicians. Five scenarios were developed to represent both realistic and ideal, interesting, situations.

The model was developed using the SocLab platform—a formalization of the sociology of organizational action. It is based on previous descriptions of the game and expert knowledge. A structural analysis permits us to examine the properties of the sub-model behind each scenario. The results corroborate certain intuitions about the scenarios representing realistic cases, e.g., they indicate that publishers, being isolated in their interests, are subject to strong pressures from other actors, who have a circumstantial alliance. Administrators take an intermediate stance in all scenarios.

The best scenarios for open access are those in which Politicians and Funders clearly support the cause by expressing mandates in that direction, backing academics. Surprisingly, the model shows that it is in the Publishers’ interest not to take an extremist position against open access.

URL : Simulating and Contrasting the Game of Open Access in Diverse Cultural Contexts: A Social Simulation Model

DOI : https://doi.org/10.3390/publications11030040

Global visibility of publications through Digital Object Identifiers

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Authors : Houcemeddine Turki, Grischa Fraumann, Mohamed Ali Hadj Taieb, Mohamed Ben Aouicha

This brief research report analyzes the availability of Digital Object Identifiers (DOIs) worldwide, highlighting the dominance of large publishing houses and the need for unique persistent identifiers to increase the visibility of publications from developing countries.

The study reveals that a considerable amount of publications from developing countries are excluded from the global flow of scientific information due to the absence of DOIs, emphasizing the need for alternative publishing models.

The authors suggest that the availability of DOIs should receive more attention in scholarly communication and scientometrics, contributing to a necessary debate on DOIs relevant for librarians, publishers, and scientometricians.

URL : Global visibility of publications through Digital Object Identifiers

DOI : https://doi.org/10.3389/frma.2023.1207980

Interventions in scholarly communication: Design lessons from public health

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Authors : Micah Altman, Philip N. Cohen, Jessica Polka

Many argue that swift and fundamental interventions in the system of scholarly communication are needed. However, there are substantial disagreements over the short- and long-term benefits of most proposed approaches to changing the practice of science communication, and the lack of systematic, empirically based research in this area makes these controversies difficult to resolve. We argue that experience within public health can be usefully applied to scholarly communication.

Starting with the history of DDT (Dichlorodiphenyltrichloroethane) application, we illustrate four ways complex human systems threaten reliable predictions and blunt ad-hoc interventions. We then show how these apply to interventions in scholarly publication – open access based on the article processing charge (APC), and preprints – to yield surprising results. Finally, we offer approaches to help guide the design of future interventions: identifying measures and outcomes, developing infrastructure, incorporating assessment, and contributing to theories of systemic change.

URL : Interventions in scholarly communication: Design lessons from public health

DOI : https://doi.org/10.5210/fm.v28i8.12941

Coordinating culture change across the research landscape

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Authors : Leslie D. McIntosh, Cynthia Hudson Vitale

Scientific integrity necessitates applying scientific methods properly, collecting and analyzing data appropriately, protecting human subjects rightly, performing studies rigorously, and communicating findings transparently.

But who is responsible for upholding research integrity, mitigating misinformation, and increasing trust in science beyond individual researchers? We posit that supporting the scientific reputation requires a coordinated approach across all stakeholders: funding agencies, publishers, scholarly societies, research institutions, and journalists and media, and policy-makers.

URL : Coordinating culture change across the research landscape

DOI : https://doi.org/10.3389/frma.2023.1134082