Review
Public, Environmental & Occupational Health
Roger D. Peng, Stephanie C. Hicks
Summary: Advancements in computing technology have led to significant progress in scientific discovery, but have also raised concerns about the reproducibility of data analyses and the replicability of scientific findings. These issues highlight the importance of ensuring transparency and rigor in research practices to improve the reliability of public health research in the future.
ANNUAL REVIEW OF PUBLIC HEALTH, VOL 42, 2021
(2021)
Article
Surgery
Mona Ascha, Leila Katabi, Erica Stevens, James Gatherwright, Matthew Vassar
Summary: The aim of this study was to evaluate the reproducibility and transparency of research in the plastic surgery literature. The results showed that the majority of empirical studies in this field did not provide data availability statements or material availability statements, indicating a lack of reproducible research practices in plastic surgery.
PLASTIC AND RECONSTRUCTIVE SURGERY
(2022)
Article
Biology
Alejandro de la Vega, Roberta Rocca, Ross W. Blair, Christopher J. Markiewicz, Jeff Mentch, James D. Kent, Peer Herholz, Satrajit S. Ghosh, Russell A. Poldrack, Tal Yarkoni
Summary: Neuroscout is an end-to-end platform for analyzing naturalistic fMRI data, which automatically annotates stimuli from multiple ecologically-valid datasets and reduces the burden of reproducible research. Through validating the automatic feature extraction approach, it has the potential to support more robust fMRI research and democratize fMRI research.
Article
Multidisciplinary Sciences
Anthony Mammoliti, Petr Smirnov, Minoru Nakano, Zhaleh Safikhani, Christopher Eeles, Heewon Seo, Sisira Kadambat Nair, Arvind S. Mer, Ian Smith, Chantal Ho, Gangesh Beri, Rebecca Kusko, Eva Lin, Yihong Yu, Scott Martin, Marc Hafner, Benjamin Haibe-Kains
Summary: Reproducibility is crucial in open science for findings to be valid and shareable. The complexity and growth of biomedical data pose challenges in processing and sharing. ORCESTRA platform tackles this by processing multimodal biomedical data and providing customizable workflows.
NATURE COMMUNICATIONS
(2021)
Review
Microbiology
Matti O. Ruuskanen, Deepti Vats, Renuka Potbhare, Ameeta RaviKumar, Eveliina Munukka, Richa Ashma, Leo Lahti
Summary: Skin is a complex organ that acts as a critical barrier and regulator in interactions between the human body and its environment. Recent studies have revealed the significant role of microbial communities in maintaining the health and function of the skin and immune system. Various factors influence the composition and diversity of these communities on the skin, and specific changes in skin microbiota have been linked to the development of chronic diseases. Standardized practices in studying skin microbial communities can enhance our understanding of their structures, functions, and associations with health.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Communication
Jonathan Zong, J. Nathan Matias
Summary: The lack of consent or debriefing in online research has led to public distrust. To address this, designers need to create systems that can establish and maintain public trust in large-scale online research. The researchers designed the Bartleby system to address this issue by debriefing participants and soliciting their opinions. The study found that Bartleby addresses procedural concerns and allows participants to contribute value-driven opinions.
SOCIAL MEDIA + SOCIETY
(2022)
Article
Medicine, General & Internal
Vibeke Fosse, Emanuela Oldoni, Florence Bietrix, Alfredo Budillon, Evangelos P. Daskalopoulos, Maddalena Fratelli, Bjoern Gerlach, Peter M. A. Groenen, Sabine M. Holter, Julia M. L. Menon, Ali Mobasheri, Nikki Osborne, Merel Ritskes-Hoitinga, Bettina Ryll, Elmar Schmitt, Anton Ussi, Antonio L. Andreu, Emmet McCormack
Summary: Personalized medicine aims to provide tailor-made prevention and treatment strategies for specific groups, but there are challenges in clinical relevance and model validity. Researchers have developed a set of recommendations to improve the robustness of preclinical methods in translational research for personalized medicine through literature review, expert discussions, and consensus meetings.
Article
Biochemistry & Molecular Biology
Nicole Y. Souren, Norbert E. Fusenig, Stefanie Heck, Wilhelm G. Dirks, Amanda Capes-Davis, Franca Bianchini, Christoph Plass
Summary: Misidentification of cell lines is a serious threat to scientific reproducibility. Strict multi-layered quality control, collaborations between journals, research institutions, and funders, as well as regular authentication schemes and staff training, are essential to address this issue. Future steps should focus on enhancing good cell culture practices.
Article
Surgery
Bryan Taylor Hughes, Andrew Niemann, Daniel Tritz, Kryston Boyer, Hal Robbins, Matt Vassar
Summary: This study evaluates the transparency and reproducibility of 387 articles published in surgery journals. The majority of the studies in the sample did not meet the baseline standards of reproducibility, as they did not make their materials, protocols, data, or analysis scripts available. Conflicts of interest declarations and pre-registered studies were also rare. This highlights the need for improvement in the transparency of surgical literature.
JOURNAL OF SURGICAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Nicolas Vallet, David Michonneau, Simon Tournier
Summary: The reproducibility crisis in science urges scientists to promote transparency and open access to methods, data and source codes. However, the complexity and dependencies of computational environments remain a challenge. Tools like Guix can help scientists share their computational environments and improve transparency.
Article
Biology
Luc Cornet, Benoit Durieu, Frederik Baert, Elizabet D'hooge, David Colignon, Loic Meunier, Valerian Lupo, Ilse Cleenwerck, Heide-Marie Daniel, Leen Rigouts, Damien Sirjacobs, Stephane Declerck, Peter Vandamme, Annick Wilmotte, Denis Baurain, Pierre Becker
Summary: A bioinformatics toolbox called GEN-ERA has been developed by the Belgian Coordinated Collections of Microorganisms. It allows researchers to perform robust phylogenomic analyses on bacteria and small eukaryotes without specific training in bioinformatics. The toolbox provides workflows for genome downloading, quality assessment, contamination estimation, tree reconstruction, average nucleotide identity comparisons, and metabolic modeling. It has been tested on various microorganisms and used in a case study on Gloeobacterales for microbial taxonomy.
Article
Biology
Patrick Bodilly Kane, Jonathan Kimmelman
Summary: The Reproducibility Project: Cancer Biology aims to provide evidence on reproducibility in cancer research and identify factors influencing reproducibility. Results suggest the current diagnostic machine in cancer research recommends many non-reproducible findings for further advancement, raising concerns. However, further evaluation is needed, with unanswered questions on the machine's accuracy, societal costs of false positives and negatives, and interpretation of its outputs by scientists and others.
Article
Psychology
Kristina Wiebels, David Moreau
Summary: Containers have gained popularity in computing, software engineering, and scientific research. Despite being crucial for reproducible science, they have not yet become mainstream in psychology. This tutorial describes the logic behind containers, how to use them, practical problems they can solve, and provides examples of implementing containerization in research workflows using Docker and R.
ADVANCES IN METHODS AND PRACTICES IN PSYCHOLOGICAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Dario Righelli, Claudia Angelini
Summary: Irreproducibility has become a general problem in omics data analysis in recent years due to the use of sophisticated and poorly described computational procedures. To avoid misleading results, it is necessary to inspect and reproduce the entire data analysis. Reproducible Research provides guidelines for public access to analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce findings.
Review
Biochemical Research Methods
Stephan Fischer, Megan Crow, Benjamin D. Harris, Jesse Gillis
Summary: The protocol introduces an efficient and robust quantification method for cell-type replicability using MetaNeighbor, which allows for identification of gene sets contributing to cell identity. The method is based on an open-source R package and can typically be run in less than 5 minutes for millions of cells.