scholarly journals Open science practices and risks arising from misuse of biological research

2021 ◽  
Author(s):  
James Andrew Smith ◽  
Jonas Sandbrink
Keyword(s):  
Risk Mitigation ◽  
Open Data ◽  
Open Science ◽  
Biological Research ◽  
Science Practices ◽  
Societal Benefit ◽  
General Importance ◽  
Science Community ◽  
Application Programming ◽  
Programming Interfaces

The proliferation of open science may inadvertently increase the chance of deliberate or accidental misuse of research. Here, we examine the interaction between open science practices and biosecurity and biosafety to identify risks and opportunities for risk mitigation. We argue that open data, code, and materials may increase risks from research with misuse potential, despite their general importance. For instance, increased access to protocols, datasets, and computational methods for viral engineering may increase the risk of release of enhanced pathogens. For this dangerous subset of research, both open science and biosecurity goals may be achieved by using access-controlled repositories or application programming interfaces. The increased use of preprints could challenge any strategy for risk mitigation that relies on assessment at the publication stage, emphasising the need for earlier oversight in the research lifecycle. Preregistration of research, a practice promoted by the open science community, provides an opportunity for achieving biosecurity risk assessment at the conception of research. Open science and biosecurity experts have an important role to play in enabling responsible research with maximal societal benefit.

scholarly journals Recommendations for an Open Science approach to welding process research data

2021 ◽  
Author(s):  
Cagtay Fabry ◽  
Andreas Pittner ◽  
Volker Hirthammer ◽  
Michael Rethmeier
Keyword(s):  
Domain Knowledge ◽  
Knowledge Exchange ◽  
Welding Process ◽  
Open Science ◽  
Research Data ◽  
Fusion Welding ◽  
File Format ◽  
Data Format ◽  
Science Practices ◽  
Science Community

AbstractThe increasing adoption of Open Science principles has been a prevalent topic in the welding science community over the last years. Providing access to welding knowledge in the form of complex and complete datasets in addition to peer-reviewed publications can be identified as an important step to promote knowledge exchange and cooperation. There exist previous efforts on building data models specifically for fusion welding applications; however, a common agreed upon implementation that is used by the community is still lacking. One proven approach in other domains has been the use of an openly accessible and agreed upon file and data format used for archiving and sharing domain knowledge in the form of experimental data. Going into a similar direction, the welding community faces particular practical, technical, and also ideological challenges that are discussed in this paper. Collaboratively building upon previous work with modern tools and platforms, the authors motivate, propose, and outline the use of a common file format specifically tailored to the needs of the welding research community as a complement to other already established Open Science practices. Successfully establishing a culture of openly accessible research data has the potential to significantly stimulate progress in welding research.

scholarly journals Learning Open Science by doing Open Science. A reflection of a qualitative research project-based seminar

2020 ◽  
Vol 36 (3) ◽  
pp. 263-279
Author(s):  
Isabel Steinhardt
Keyword(s):  
Qualitative Research ◽  
Open Source ◽  
Knowledge Society ◽  
Open Data ◽  
Open Science ◽  
Research Project ◽  
Science Practices ◽  
Bachelor's Degrees ◽  
Participatory Technologies ◽  
Digital Knowledge

Openness in science and education is increasing in importance within the digital knowledge society. So far, less attention has been paid to teaching Open Science in bachelor’s degrees or in qualitative methods. Therefore, the aim of this article is to use a seminar example to explore what Open Science practices can be taught in qualitative research and how digital tools can be involved. The seminar focused on the following practices: Open data practices, the practice of using the free and open source tool “Collaborative online Interpretation, the practice of participating, cooperating, collaborating and contributing through participatory technologies and in social (based) networks. To learn Open Science practices, the students were involved in a qualitative research project about “Use of digital technologies for the study and habitus of students”. The study shows the practices of Open Data are easy to teach, whereas the use of free and open source tools and participatory technologies for collaboration, participation, cooperation and contribution is more difficult. In addition, a cultural shift would have to take place within German universities to promote Open Science practices in general.

scholarly journals Open Developmental Science: An Overview and Annotated Reading List

2021 ◽  
Author(s):  
Tamara Kalandadze ◽  
Sara Ann Hart
Keyword(s):  
Open Access ◽  
Open Data ◽  
Open Science ◽  
Science Practices ◽  
The Core ◽  
Reading List ◽  
Annotated List ◽  
Developmental Science ◽  
Starting Point

The increasing adoption of open science practices in the last decade has been changing the scientific landscape across fields. However, developmental science has been relatively slow in adopting open science practices. To address this issue, we followed the format of Crüwell et al., (2019) and created summaries and an annotated list of informative and actionable resources discussing ten topics in developmental science: Open science; Reproducibility and replication; Open data, materials and code; Open access; Preregistration; Registered reports; Replication; Incentives; Collaborative developmental science.This article offers researchers and students in developmental science a starting point for understanding how open science intersects with developmental science. After getting familiarized with this article, the developmental scientist should understand the core tenets of open and reproducible developmental science, and feel motivated to start applying open science practices in their workflow.

scholarly journals OpenFDA: an innovative platform providing access to a wealth of FDA’s publicly available data

2015 ◽  
Vol 23 (3) ◽  
pp. 596-600 ◽  
Author(s):  
Taha A Kass-Hout ◽  
Zhiheng Xu ◽  
Matthew Mohebbi ◽  
Hans Nelsen ◽  
Adam Baker ◽  
...  
Keyword(s):  
Open Data ◽  
The United States ◽  
Important Food ◽  
The Public ◽  
New Public ◽  
Application Programming ◽  
Public Datasets ◽  
Programming Interfaces ◽  
Apparent Association

Objective The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Materials and Methods Using cutting-edge technologies deployed on FDA’s new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Results Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. Conclusion With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products.

scholarly journals Born-Open Data for E-Prime

2020 ◽  
Author(s):  
Denis Cousineau
Keyword(s):  
Open Access ◽  
Open Data ◽  
Open Science ◽  
Research Community ◽  
Data Repository ◽  
Data Frame ◽  
Science Practices ◽  
Data Practices ◽  
Data Files ◽  
Access Data

Born-Open Data experiments are encouraged for better open science practices. To be adopted, Born-Open data practices must be easy to implement. Herein, I introduce a package for E-Prime such that the data files are automatically saved on a GitHub repository. The BornOpenData package for E-Prime works seamlessly and performs the upload as soon as the experiment is finished so that there is no additional steps to perform beyond placing a package call within E-Prime. Because E-Prime files are not standard tab-separated files, I also provide an R function that retrieves the data directly from GitHub into a data frame ready to be analyzed. At this time, there are no standards as to what should constitute an adequate open-access data repository so I propose a few suggestions that any future Born-Open data system could follow for easier use by the research community.

scholarly journals ‘Trust Us’: Open Data and Preregistration in Political Science and International Relations

2022 ◽  
Author(s):  
Bermond Scoggins ◽  
Matthew Peter Robertson
Keyword(s):  
International Relations ◽  
Political Science ◽  
Statistical Inference ◽  
Large Scale ◽  
Open Data ◽  
Population Level ◽  
Open Science ◽  
Science Practices ◽  
Level Data ◽  
Replication Crisis

The scientific method is predicated on transparency -- yet the pace at which transparent research practices are being adopted by the scientific community is slow. The replication crisis in psychology showed that published findings employing statistical inference are threatened by undetected errors, data manipulation, and data falsification. To mitigate these problems and bolster research credibility, open data and preregistration have increasingly been adopted in the natural and social sciences. While many political science and international relations journals have committed to implementing these reforms, the extent of open science practices is unknown. We bring large-scale text analysis and machine learning classifiers to bear on the question. Using population-level data -- 93,931 articles across the top 160 political science and IR journals between 2010 and 2021 -- we find that approximately 21% of all statistical inference papers have open data, and 5% of all experiments are preregistered. Despite this shortfall, the example of leading journals in the field shows that change is feasible and can be effected quickly.

scholarly journals Accelerating open science: The collaborative replications and education project (CREP)

2018 ◽  
Author(s):  
Gerit Pfuhl ◽  
Jon Grahe
Keyword(s):  
Behavioral Science ◽  
Research Training ◽  
Meta Analysis ◽  
Academic Research ◽  
Open Data ◽  
Open Science ◽  
Open Access Publishing ◽  
Quality Data ◽  
Education Project ◽  
Science Practices

Watch the VIDEO.Recent years have seen a revolution in publishing, and large support for open access publishing. There has been a slower acceptance and transition to other open science principles such as open data, open materials, and preregistration. To accelerate the transition and make open science the new standard, the collaborative replications and education project (CREP; http://osf.io/wfc6u/)) was launched in 2013, hosted on the Open Science Framework (osf.io). OSF is like a preprint, collecting partial data with each individual contributors project. CREP introduces open science at the start of academic research, facilitating student research training in open science and solidifying behavioral science results. The CREP team attempts to achieve this by inviting contributors to replicate one of several replication studies selected for scientific impact and suitability for undergraduates to complete during one academic term. Contributors follow clear protocols with students interacting with a CREP team that reviews the materials and video of the procedure to ensure quality data collection while students are learning science practices and methods. By combining multiple replications from undergraduates across the globe, the findings can be pooled to conduct meta-analysis and so contribute to generalizable and replicable research findings. CREP is careful to not interpret any single result. CREP has recently joined forces with the psychological science accelerator (PsySciAcc), a globally distributed network of psychological laboratories accelerating the accumulation of reliable and generalizable results in the behavioral sciences. The Department of Psychology at UiT is part of the network and has two ongoing CREP studies, maintaining open science practices early on. In this talk, we will present our experiences of conducting transparent replicable research, and experience with preprints from a supervisor and researcher perspective.

scholarly journals Preregistration specificity & adherence: A review of preregistered gambling studies & cross-disciplinary comparison

2021 ◽  
Author(s):  
Robert Heirene ◽  
Debi LaPlante ◽  
Eric R. Louderback ◽  
Brittany Keen ◽  
Marjan Bakker ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Open Data ◽  
Open Science ◽  
Eligibility Criteria ◽  
Science Practices ◽  
Methodological Choices ◽  
The Mean ◽  
The Many ◽  
Practical Recommendations ◽  
Current Practices

Study preregistration is one of several “open science” practices (e.g., open data, preprints) that researchers use to improve the transparency and rigour of their research. As more researchers adopt preregistration as a regular research practice, examining the nature and content of preregistrations can help identify strengths and weaknesses of current practices. The value of preregistration, in part, relates to the specificity of the study plan and the extent to which investigators adhere to this plan. We identified 53 preregistrations from the gambling studies field meeting our predefined eligibility criteria and scored their level of specificity using a 23-item protocol developed to measure the extent to which a clear and exhaustive preregistration plan restricts various researcher degrees of freedom (RDoF; i.e., the many methodological choices available to researchers when collecting and analysing data, and when reporting their findings). We also scored studies on a 32-item protocol that measured adherence to the preregistered plan in the study manuscript. We found that gambling preregistrations had low specificity levels on most RDoF. However, a comparison with a sample of cross-disciplinary preregistrations (N = 52; Bakker et al., 2020) indicated that gambling preregistrations scored higher on 12 (of 29) items. Thirteen (65%) of the 20 associated published articles or preprints deviated from the protocol without declaring as much (the mean number of undeclared deviations per article was 2.25, SD = 2.34). Overall, while we found improvements in specificity and adherence over time (2017-2020), our findings suggest the purported benefits of preregistration—including increasing transparency and reducing RDoF—are not fully achieved by current practices. Using our findings, we provide 10 practical recommendations that can be used to support and refine preregistration practices.

scholarly journals Evidence on Research Transparency in Economics

2021 ◽  
Vol 35 (3) ◽  
pp. 193-214
Author(s):  
Edward Miguel
Keyword(s):  
Social Science ◽  
Open Data ◽  
Open Science ◽  
Science Practices ◽  
Radar Screen ◽  
Rapid Transition ◽  
Research Transparency ◽  
Journal Policies ◽  
Economics Research

A decade ago, the term “research transparency” was not on economists' radar screen, but in a few short years a scholarly movement has emerged to bring new open science practices, tools and norms into the mainstream of our discipline. The goal of this article is to lay out the evidence on the adoption of these approaches – in three specific areas: open data, pre-registration and pre-analysis plans, and journal policies – and, more tentatively, begin to assess their impacts on the quality and credibility of economics research. The evidence to date indicates that economics (and related quantitative social science fields) are in a period of rapid transition toward new transparency-enhancing norms. While solid data on the benefits of these practices in economics is still limited, in part due to their relatively recent adoption, there is growing reason to believe that critics' worst fears regarding onerous adoption costs have not been realized. Finally, the article presents a set of frontier questions and potential innovations.

scholarly journals Attitudes and practices of open data, preprinting, and peer-review—A cross sectional study on Croatian scientists

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0244529
Author(s):  
Ksenija Baždarić ◽  
Iva Vrkić ◽  
Evgenia Arh ◽  
Martina Mavrinac ◽  
Maja Gligora Marković ◽  
...  
Keyword(s):  
Peer Review ◽  
Open Data ◽  
Open Science ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
Demographic Information ◽  
Cross Sectional ◽  
Science Practices ◽  
Attitudes And Practices ◽  
Item Questionnaire

Attitudes towards open peer review, open data and use of preprints influence scientists’ engagement with those practices. Yet there is a lack of validated questionnaires that measure these attitudes. The goal of our study was to construct and validate such a questionnaire and use it to assess attitudes of Croatian scientists. We first developed a 21-item questionnaire called Attitudes towards Open data sharing, preprinting, and peer-review (ATOPP), which had a reliable four-factor structure, and measured attitudes towards open data, preprint servers, open peer-review and open peer-review in small scientific communities. We then used the ATOPP to explore attitudes of Croatian scientists (n = 541) towards these topics, and to assess the association of their attitudes with their open science practices and demographic information. Overall, Croatian scientists’ attitudes towards these topics were generally neutral, with a median (Md) score of 3.3 out of max 5 on the scale score. We also found no gender (P = 0.995) or field differences (P = 0.523) in their attitudes. However, attitudes of scientist who previously engaged in open peer-review or preprinting were higher than of scientists that did not (Md 3.5 vs. 3.3, P<0.001, and Md 3.6 vs 3.3, P<0.001, respectively). Further research is needed to determine optimal ways of increasing scientists’ attitudes and their open science practices.

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