About the Authors

Saskia Hiltemann

Contributed equally to this work with: Saskia Hiltemann, Helena Rasche

Roles Conceptualization, Funding acquisition, Methodology, Project administration, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliation Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands

Helena Rasche

Contributed equally to this work with: Saskia Hiltemann, Helena Rasche

Roles Conceptualization, Funding acquisition, Methodology, Project administration, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

Affiliations Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands, Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany, Academie voor de Technologie van Gezondheid en Milieu, Avans Hogeschool, Breda, the Netherlands

Simon Gladman

† Deceased.

Roles Software, Supervision, Validation

Affiliation Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia

Hans-Rudolf Hotz

Roles Conceptualization, Software, Validation, Writing – original draft, Writing – review & editing

Affiliations Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, SIB Swiss Institute of Bioinformatics, Basel, Switzerland

Delphine Larivière

Roles Software, Validation

Affiliation Eberly College of Science, Pennsylvania State University, State College, Pennsylvania, United States of America

Daniel Blankenberg

Roles Software, Supervision, Validation, Writing – original draft, Writing – review & editing

Affiliation Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America

Pratik D. Jagtap

Roles Funding acquisition, Software, Validation, Writing – review & editing

Affiliation Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America

Thomas Wollmann

Roles Software, Validation

Affiliation Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany

Anthony Bretaudeau

Roles Software, Validation

Affiliations IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France, GenOuest Core Facility, Univ Rennes, Inria, CNRS, IRISA, Rennes, France

Nadia Goué

Roles Software, Validation, Writing – review & editing

Affiliation AuBi, Mesocenter, Clermont Auvergne University, Aubière, France

Timothy J. Griffin

Roles Validation, Writing – review & editing

Affiliation Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America

Coline Royaux

Roles Software, Validation, Writing – original draft, Writing – review & editing

Affiliation PNDB French Biodiversity e-infrastructure, PatriNat, French Museum of Natural History, Concarneau, France

Yvan Le Bras

Roles Project administration, Software, Validation

Affiliation PNDB French Biodiversity e-infrastructure, PatriNat, French Museum of Natural History, Concarneau, France

Subina Mehta

Roles Software, Validation

Affiliation Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America

Anna Syme

Roles Software

Affiliation Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia

Frederik Coppens

Roles Funding acquisition, Validation

Affiliations Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium, VIB Center for Plant Systems Biology, Ghent, Belgium

Bert Droesbeke

Roles Software, Writing – review & editing

Affiliations Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium, VIB Center for Plant Systems Biology, Ghent, Belgium

Nicola Soranzo

Roles Software, Validation, Writing – original draft, Writing – review & editing

Affiliation Earlham Institute, Norwich Research Park, Norwich, United Kingdom

Wendi Bacon

Roles Software, Validation

Affiliation School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom

Fotis Psomopoulos

Roles Software, Validation

Affiliation Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece

Cristóbal Gallardo-Alba

Roles Software, Validation, Writing – review & editing

Affiliation Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany

John Davis

Roles Software, Validation, Writing – review & editing

Affiliation Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America

Melanie Christine Föll

Roles Software, Validation, Writing – review & editing

Affiliations Institute for Surgical Pathology, Medical Center—University of Freiburg, Faculty of Medicine, Freiburg, Germany, Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts, United States of America, German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany

Matthias Fahrner

Roles Software, Validation, Writing – review & editing

Affiliations Institute for Surgical Pathology, Medical Center—University of Freiburg, Faculty of Medicine, Freiburg, Germany, German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany

Maria A. Doyle

Roles Software, Validation

Affiliations Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia

Beatriz Serrano-Solano

Roles Software, Validation, Writing – review & editing

Affiliations Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany, ELIXIR Germany, Institute of Bio- and Geosciences (IBG-5)—Computational Metagenomics, Forschungszentrum Jülich GmbH, Jülich, Germany, Euro-BioImaging ERIC Bio-Hub, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

Anne Claire Fouilloux

Roles Software, Validation

Affiliation Simula Research Laboratory, Oslo, Norway

Peter van Heusden

Roles Software, Validation, Writing – review & editing

Affiliation South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa

Wolfgang Maier

Roles Software, Validation

Affiliation Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany

Dave Clements

Roles Conceptualization, Funding acquisition, Supervision

Affiliation Anaconda Inc, Austin, Texas, United States of America

Florian Heyl

Roles Conceptualization, Formal analysis, Software, Validation, Writing – review & editing

Affiliation Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany

Galaxy Training Network

Membership list can be found in the Acknowledgments section.

Björn Grüning

Roles Conceptualization, Formal analysis, Funding acquisition, Software, Validation, Writing – review & editing

‡ BG and BB also contributed equally to this work.

Affiliation Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany

Bérénice Batut

Roles Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

berenice.batut@gmail.com

‡ BG and BB also contributed equally to this work.

Affiliation Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany

Competing Interests

We have read the journal’s policy and the authors of this manuscript have the following competing interests: DB has a significant financial interest in GalaxyWorks, a company that may have a commercial interest in the results of this research and technology. This potential conflict of interest has been reviewed and is managed by the Cleveland Clinic. This does not alter our adherence to all the PLOS Computational Biology policies on sharing data and materials.