Journal Article Preprint Epublish 2 citations
PubMed: 39764400
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods.
ArXiv
Authors: Ziv Yaniv, Ifeanyichukwu U Anidi, Leanne Arakkal, Armando J Arroyo-Mejías, Rebecca T Beuschel, Katy Börner, Colin J Chu, Beatrice Clark, Menna R Clatworthy, Jake Colautti, Fabian Coscia, Joshua Croteau, Saven Denha, Rose Dever, Walderez O Dutra, Sonja Fritzsche, Spencer Fullam, Michael Y Gerner, Anita Gola, Kenneth J Gollob, Jonathan M Hernandez, Jyh Liang Hor, Hiroshi Ichise, Zhixin Jing, Danny Jonigk, Evelyn Kandov, Wolfgang Kastenmüller, Joshua F E Koenig, Aanandita Kothurkar, Rosa K Kortekaas, Alexandra Y Kreins, Ian T Lamborn, Yuri Lin, Katia Luciano Pereira Morais, Aleksandra Lunich, Jean C S Luz, Ryan B MacDonald, Chen Makranz, Vivien I Maltez, John E McDonough, Ryan V Moriarty, Juan M Ocampo-Godinez, Vitoria M Olyntho, Annette Oxenius, Kartika Padhan, Kirsten Remmert, Nathan Richoz, Edward C Schrom, Wanjing Shang, Lihong Shi … and 11 other authors
Affiliations
- Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Critical Care Medicine and Pulmonary Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
- UCL Institute of Ophthalmology and NIHR Moorfields Biomedical Research Centre, London, UK.
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Molecular Immunity Unit, Laboratory of Molecular Biology, Cambridge, UK.
- McMaster Immunology Research Centre, Schroeder Allergy and Immunology Research Institute, Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
- Department of Business Development, BioLegend Inc. San Diego, CA, USA.
- Functional Immunogenomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- Laboratory of Cell-Cell Interactions, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
- Division of Rheumatology, Rush University Medical Center, Chicago, IL, USA.
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA.
- Center for Research in Immuno-oncology (CRIO), Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil.
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- Institute of Pathology, Aachen Medical University, RWTH Aachen, Aachen, Germany.
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
- Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, St Joseph's Healthcare, Hamilton, ON, Canada.
- Infection Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, UK.
- Viral Vector Laboratory, Cancer Institute of São Paulo, University of São Paulo, SP, Brazil.
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Developmental Biology, Northwestern University, Chicago, IL, USA.
- Laboratorio de Bioingeniería de Tejidos, Departamento de Estudios de Posgrado e Investigación, Universidad Nacional Autónoma de México, Mexico City, Mexico.
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Center for Advanced Tissue Imaging Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Abstract
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.
MeSH
Research, Knowledge Bases, Software, Physical Exertion, Community Resources