Reproducibility2020: Progress and priorities

Authors : Leonard P. Freedman, Gautham Venugopalan, Rosann Wisman

The preclinical research process is a cycle of idea generation, experimentation, and reporting of results. The biomedical research community relies on the reproducibility of published discoveries to create new lines of research and to translate research findings into therapeutic applications.

Since 2012, when scientists from Amgen reported that they were able to reproduce only 6 of 53 “landmark” preclinical studies, the biomedical research community began discussing the scale of the reproducibility problem and developing initiatives to address critical challenges.

Global Biological Standards Institute (GBSI) released the “Case for Standards” in 2013, one of the first comprehensive reports to address the rising concern of irreproducible biomedical research.

Further attention was drawn to issues that limit scientific self-correction, including reporting and publication bias, underpowered studies, lack of open access to methods and data, and lack of clearly defined standards and guidelines in areas such as reagent validation.

To evaluate the progress made towards reproducibility since 2013, GBSI identified and examined initiatives designed to advance quality and reproducibility. Through this process, we identified key roles for funders, journals, researchers and other stakeholders and recommended actions for future progress. This paper describes our findings and conclusions.

URL : Reproducibility2020: Progress and priorities


Replicability and Reproducibility in Comparative Psychology

Author : Jeffrey R. Stevens

Psychology faces a replication crisis. The Reproducibility Project: Psychology sought to replicate the effects of 100 psychology studies. Though 97% of the original studies produced statistically significant results, only 36% of the replication studies did so (Open Science Collaboration, 2015).

This inability to replicate previously published results, however, is not limited to psychology (Ioannidis, 2005). Replication projects in medicine (Prinz et al., 2011) and behavioral economics (Camerer et al., 2016) resulted in replication rates of 25 and 61%, respectively, and analyses in genetics (Munafò, 2009) and neuroscience (Button et al., 2013) question the validity of studies in those fields. Science, in general, is reckoning with challenges in one of its basic tenets: replication.

Comparative psychology also faces the grand challenge of producing replicable research. Though social psychology has born the brunt of most of the critique regarding failed replications, comparative psychology suffers from some of the same problems faced by social psychology (e.g., small sample sizes).

Yet, comparative psychology follows the methods of cognitive psychology by often using within-subjects designs, which may buffer it from replicability problems (Open Science Collaboration, 2015). In this Grand Challenge article, I explore the shared and unique challenges of and potential solutions for replication and reproducibility in comparative psychology.

URL : Replicability and Reproducibility in Comparative Psychology

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Experiences in integrated data and research object publishing using GigaDB

Authors : Scott C Edmunds, Peter Li, Christopher I Hunter, Si Zhe Xiao, Robert L Davidson, Nicole Nogoy, Laurie Goodman

In the era of computation and data-driven research, traditional methods of disseminating research are no longer fit-for-purpose. New approaches for disseminating data, methods and results are required to maximize knowledge discovery.

The “long tail” of small, unstructured datasets is well catered for by a number of general-purpose repositories, but there has been less support for “big data”. Outlined here are our experiences in attempting to tackle the gaps in publishing large-scale, computationally intensive research.

GigaScience is an open-access, open-data journal aiming to revolutionize large-scale biological data dissemination, organization and re-use. Through use of the data handling infrastructure of the genomics centre BGI, GigaScience links standard manuscript publication with an integrated database (GigaDB) that hosts all associated data, and provides additional data analysis tools and computing resources.

Furthermore, the supporting workflows and methods are also integrated to make published articles more transparent and open. GigaDB has released many new and previously unpublished datasets and data types, including as urgently needed data to tackle infectious disease outbreaks, cancer and the growing food crisis.

Other “executable” research objects, such as workflows, virtual machines and software from several GigaScience articles have been archived and shared in reproducible, transparent and usable formats.

With data citation producing evidence of, and credit for, its use in the wider research community, GigaScience demonstrates a move towards more executable publications. Here data analyses can be reproduced and built upon by users without coding backgrounds or heavy computational infrastructure in a more democratized manner.

URL : Experiences in integrated data and research object publishing using GigaDB


Open Science: What, Why, and How

Authors : Barbara A. Spellman, Elizabeth A. Gilbert, Katherine S. Corker

Open Science is a collection of actions designed to make scientific processes more transparent and results more accessible. Its goal is to build a more replicable and robust science; it does so using new technologies, altering incentives, and changing attitudes.

The current movement towards open science was spurred, in part, by a recent “series of unfortunate events” within psychology and other sciences.

These events include the large number of studies that have failed to replicate and the prevalence of common research and publication procedures that could explain why.

Many journals and funding agencies now encourage, require, or reward some open science practices, including pre-registration, providing full materials, posting data, distinguishing between exploratory and confirmatory analyses, and running replication studies.

Individuals can practice and encourage open science in their many roles as researchers, authors, reviewers, editors, teachers, and members of hiring, tenure, promotion, and awards committees.

A plethora of resources are available to help scientists, and science, achieve these goals.


Transparency: the emerging third dimension of Open Science and Open Data

This paper presents an exploration of the concept of research transparency. The policy context is described and situated within the broader arena of open science. This is followed by commentary on transparency within the research process, which includes a brief overview of the related concept of reproducibility and the associated elements of research integrity, fraud and retractions.

A two-dimensional model or continuum of open science is considered and the paper builds on this foundation by presenting a three-dimensional model, which includes the additional axis of ‘transparency’. The concept is further unpacked and preliminary definitions of key terms are introduced: transparency, transparency action, transparency agent and transparency tool.

An important linkage is made to the research lifecycle as a setting for potential transparency interventions by libraries. Four areas are highlighted as foci for enhanced engagement with transparency goals: Leadership and Policy, Advocacy and Training, Research Infrastructures and Workforce Development.


Reproducible Research Practices and Transparency across the Biomedical Literature

There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest.

In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of 441 biomedical journal articles published in 2000–2014. Only one study provided a full protocol and none made all raw data directly available. Replication studies were rare (n = 4), and only 16 studies had their data included in a subsequent systematic review or meta-analysis. The majority of studies did not mention anything about funding or conflicts of interest.

The percentage of articles with no statement of conflict decreased substantially between 2000 and 2014 (94.4% in 2000 to 34.6% in 2014); the percentage of articles reporting statements of conflicts (0% in 2000, 15.4% in 2014) or no conflicts (5.6% in 2000, 50.0% in 2014) increased.

Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding. This study provides baseline data to compare future progress in improving these indicators in the scientific literature.

URL : Reproducible Research Practices and Transparency across the Biomedical Literature

DOI : 10.1371/journal.pbio.1002333

Reproducibility, Correctness, and Buildability: the Three Principles for Ethical Public Dissemination of Computer Science and Engineering Research

« We propose a system of three principles of public dissemination, which we call reproducibility, correctness, and buildability, and make the argument that consideration of these principles is a necessary step when publicly disseminating results in any evidence-based scientific or engineering endeavor. We examine how these principles apply to the release and disclosure of the four elements associated with computer science research: theory, algorithms, code, and data. Reproducibility refers to the capability to reproduce fundamental results from released details. Correctness refers to the ability of an independent reviewer to verify and validate the results of a paper. We introduce the new term buildability to indicate the ability of other researchers to use the published research as a foundation for their own new work. This is more broad than extensibility, as it requires that the published results have reached a level of completeness that the research can be used for its stated purpose, and has progressed beyond the level of a preliminary idea. We argue that these three principles are not being sufficiently met by current publications and proposals in computer science and engineering, and represent a goal for which publishing should continue to aim. We introduce standards for the evaluation of reproducibility, correctness, and buildability in relation to the varied elements of computer science research and discuss how they apply to proposals, workshops, conferences, and journal publications, making arguments for appropriate standards of each principle in these settings. We address modern issues including big data, data confidentiality, privacy, security, and privilege. Our examination raises questions for discussion in the community on the appropriateness of publishing works that fail to meet one, some, or all of the stated principles. »