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van Kampen AHC, Mahamune U, Jongejan A, van Schaik BDC, Balashova D, Lashgari D, Pras-Raves M, Wever EJM, Dane AD, García-Valiente R, Moerland PD. ENCORE: a practical implementation to improve reproducibility and transparency of computational research. Nat Commun 2024; 15:8117. [PMID: 39284801 PMCID: PMC11405857 DOI: 10.1038/s41467-024-52446-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 09/06/2024] [Indexed: 09/20/2024] Open
Abstract
Reproducibility of computational research is often challenging despite established guidelines and best practices. Translating these guidelines into practical applications remains difficult. Here, we present ENCORE, an approach to enhance transparency and reproducibility by guiding researchers in how to structure and document a computational project. ENCORE builds on previous efforts in computational reproducibility and integrates all project components into a standardized file system structure. It utilizes pre-defined files as documentation templates, leverages GitHub for software versioning, and includes an HTML-based navigator. ENCORE is designed to be agnostic to the type of computational project, data, programming language, and ICT infrastructure, and does not rely on specific software tools. We also share our group's experience using ENCORE, highlighting that the most significant challenge to the routine adoption of approaches like ours is the lack of incentives to motivate researchers to dedicate sufficient time and effort to ensure reproducibility.
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Affiliation(s)
- Antoine H C van Kampen
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands.
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands.
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, Netherlands.
| | - Utkarsh Mahamune
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Aldo Jongejan
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
| | - Barbera D C van Schaik
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Daria Balashova
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Danial Lashgari
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Mia Pras-Raves
- Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Meibergdreef 9, Amsterdam, Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
| | - Eric J M Wever
- Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Meibergdreef 9, Amsterdam, Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
| | - Adrie D Dane
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
| | - Rodrigo García-Valiente
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Perry D Moerland
- Amsterdam UMC, University of Amsterdam, Bioinformatics Laboratory, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Netherlands. Amsterdam Public Health, Methodology, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
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Mudumbai SC, Gabriel RA, Howell S, Tan JM, Freundlich RE, O’Reilly Shah V, Kendale S, Poterack K, Rothman BS. Public Health Informatics and the Perioperative Physician: Looking to the Future. Anesth Analg 2024; 138:253-272. [PMID: 38215706 PMCID: PMC10825795 DOI: 10.1213/ane.0000000000006649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
The role of informatics in public health has increased over the past few decades, and the coronavirus disease 2019 (COVID-19) pandemic has underscored the critical importance of aggregated, multicenter, high-quality, near-real-time data to inform decision-making by physicians, hospital systems, and governments. Given the impact of the pandemic on perioperative and critical care services (eg, elective procedure delays; information sharing related to interventions in critically ill patients; regional bed-management under crisis conditions), anesthesiologists must recognize and advocate for improved informatic frameworks in their local environments. Most anesthesiologists receive little formal training in public health informatics (PHI) during clinical residency or through continuing medical education. The COVID-19 pandemic demonstrated that this knowledge gap represents a missed opportunity for our specialty to participate in informatics-related, public health-oriented clinical care and policy decision-making. This article briefly outlines the background of PHI, its relevance to perioperative care, and conceives intersections with PHI that could evolve over the next quarter century.
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Affiliation(s)
- Seshadri C. Mudumbai
- Anesthesiology and Perioperative Care Service, Veterans Affairs Palo Alto Health Care System
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine
| | - Rodney A. Gabriel
- Department of Anesthesiology, University of California, San Diego, California
| | | | - Jonathan M. Tan
- Department of Anesthesiology Critical Care Medicine, Children’s Hospital Los Angeles
- Department of Anesthesiology, Keck School of Medicine at the University of Southern California
- Spatial Sciences Institute at the University of Southern California
| | - Robert E. Freundlich
- Department of Anesthesiology, Surgery, and Biomedical Informatics, Vanderbilt University Medical Center
| | | | - Samir Kendale
- Department of Anesthesia, Critical Care and Pain Medicine, Beth Israel Deaconess Medical Center
| | - Karl Poterack
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic
| | - Brian S. Rothman
- Department of Anesthesiology, Surgery, and Biomedical Informatics, Vanderbilt University Medical Center
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