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Bioconda: A sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S Pedersen, Youri Hoogstrate, Anthony Bretaudeau, Devon Ryan, Gildas Le Corguillé, Dilmurat Yusuf, Sebastian Luna-Valero, Rory Kirchner, Karel Brinda, Thomas Wollmann, Martin Raden, Simon J. van Heeringen, Nicola Soranzo, Lorena Pantano, Zachary Charlop-Powers, Per Unneberg, Matthias De Smet, Marcel Martin, Greg Von Kuster, Tiago Antao, Milad Miladi, Kevin Thornton, Christian Brueffer, Marius van den Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, K´evin Gravouil, Joachim Wolff, Manuel Holtgrewe, Jörg Fallmann, Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif, Philip Mabon, Xiao-Ou Zhang, Wei Shen, Jennifer Cabral, Cristel Thomas, Eric Enns, Joseph Brown, Jorrit Boekel, Mattias de Hollander, Jerome Kelleher, Nitesh Turaga, Julian R. de Ruiter, Dave Bouvier, Simon Gladman, Saket Choudhary, Nicholas Harding, Florian Eggenhofer, Arne Kratz, Zhuoqing Fang, Robert Kleinkauf, Henning Timm, Peter J. A. Cock, Enrico Seiler, Colin Brislawn, Hai Nguyen, Endre Bakken Stovner, Philip Ewels, Matt Chambers, James E. Johnson, Emil Hägglund, Simon Ye, Roman Valls Guimera, Elmar Pruesse, W. Augustine Dunn, Lance Parsons, Rob Patro, David Koppstein, Elena Grassi, Inken Wohlers, Alex Reynolds, MacIntosh Cornwell, Nicholas Stoler, Daniel Blankenberg, Guowei He, Marcel Bargull, Alexander Junge, Rick Farouni, Mallory Freeberg, Sourav Singh, Daniel R. Bogema, Fabio Cumbo, Liang-Bo Wang, David E Larson, Matthew L. Workentine, Upendra Kumar Devisetty, Sacha Laurent, Pierrick Roger, Xavier Garnier, Rasmus Agren, Aziz Khan, John M Eppley, Wei Li, Bianca Katharina Stöcker, Tobias Rausch, James Taylor, Patrick R. Wright, Adam P. Taranto, Davide Chicco, Bengt Sennblad, Jasmijn A. Baaijens, Matthew Gopez, Nezar Abdennur, Iain Milne, Jens Preussner, Luca Pinello, Avi Srivastava, Aroon T. Chande, Philip Reiner Kensche, Yuri Pirola, Michael Knudsen, Ino de Bruijn, Kai Blin, Giorgio Gonnella, Oana M. Enache, Vivek Rai, Nicholas R. Waters, Saskia Hiltemann, Matthew L. Bendall, Christoph Stahl, Alistair Miles, Yannick Boursin, Yasset Perez-Riverol, Sebastian Schmeier, Erik Clarke, Kevin Arvai, Matthieu Jung, Tom´as Di Domenico, Julien Seiler, Eric Rasche, Etienne Kornobis, Daniela Beisser, Sven Rahmann, Alexander S Mikheyev, Camy Tran, Jordi Capellades, Christopher Schröder, Adrian Emanuel Salatino, Simon Dirmeier, Timothy H. Webster, Oleksandr Moskalenko, Gordon Stephen, Johannes Köster
doi: https://doi.org/10.1101/207092
Björn Grüning
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Ryan Dale
2Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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Andreas Sjödin
3Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Ume˚a. Sweden
4Department of Chemistry, Computational Life Science Cluster (CLiC), Ume˚a University, Ume˚a, Sweden
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Brad A. Chapman
5Harvard T.H. Chan School of Public Health, Boston, United States
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Jillian Rowe
6NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
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Christopher H. Tomkins-Tinch
7Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
8Broad Institute of MIT and Harvard, Cambridge, United States
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Renan Valieris
9Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, S˜ao Paulo, Brazil
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Adam Caprez
10Holland Computing Center, University of Nebraska, Lincoln, United States
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Bérénice Batut
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Mathias Haudgaard
11Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
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Thomas Cokelaer
12Bioinformatics and Biostatistics Hub - C3BI, USR IP CNRS, Institut Pasteur, Paris, France
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Kyle A. Beauchamp
13Counsyl, South San Francisco, United States
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Brent S Pedersen
14Department of Human Genetics, University of Utah, Eccles Institute of Human Genetics, Salt Lake City
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Youri Hoogstrate
15Erasmus Medical Center, Department of Urology, Rotterdam, The Netherlands
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Anthony Bretaudeau
16INRA, UMR IGEPP, BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
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Devon Ryan
17Bioinformatics core facility, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
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Gildas Le Corguillé
18UPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, France
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Dilmurat Yusuf
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Sebastian Luna-Valero
19MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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Rory Kirchner
20Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States
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Karel Brinda
21Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States
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Thomas Wollmann
22University of Heidelberg and DKFZ, Heidelberg, Germany
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Martin Raden
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Simon J. van Heeringen
23Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
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Nicola Soranzo
24Earlham Institute, Norwich Research Park, Norwich, United Kindgom
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Lorena Pantano
5Harvard T.H. Chan School of Public Health, Boston, United States
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Zachary Charlop-Powers
25The Laboratory for Genetically Encoded Small Molecules, The Rockefeller University, New York, United States
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Per Unneberg
26Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Matthias De Smet
27Ghent University Hospital, Ghent University, Belgium
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Marcel Martin
28Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Sweden
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Greg Von Kuster
29Institute for CyberScience, Pennsylvania State University, University Park, United States
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Tiago Antao
30Division of Biological Sciences, University of Montana, Missoula, United States of America
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Milad Miladi
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Kevin Thornton
31Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, United States
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Christian Brueffer
32Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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Marius van den Beek
33Stem Cells and Tissue Homeostasis, Institut Curie, Paris, France
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Daniel Maticzka
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Clemens Blank
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Sebastian Will
34Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
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K´evin Gravouil
35Universit´e Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
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Joachim Wolff
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Manuel Holtgrewe
36Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
37Charité Universitätsmedizin Berlin, Berlin, Germany
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Jörg Fallmann
38Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
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Vitor C. Piro
39Bioinformatics Unit, Robert Koch Institute, Berlin, Germany
40CAPES Foundation, Ministry of Education of Brazil, Bras´ılia, Brazil
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Ilya Shlyakhter
8Broad Institute of MIT and Harvard, Cambridge, United States
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Ayman Yousif
41Center for Genomics and System Biology, New York University, Abu Dhabi, United Arab Emirates
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Philip Mabon
42National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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Xiao-Ou Zhang
43Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
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Wei Shen
44Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu, China
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Jennifer Cabral
42National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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Cristel Thomas
45Northrop Grumman Corporation, Technology Services, Rockville, United States
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Eric Enns
42National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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Joseph Brown
46Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
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Jorrit Boekel
47Department of Oncology-Pathology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
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Mattias de Hollander
48Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Jerome Kelleher
49Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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Nitesh Turaga
50Department of Biology, Johns Hopkins University, Baltimore, United States
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Julian R. de Ruiter
51Divisions of Molecular Pathology and Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Dave Bouvier
52Department of Biochemistry Molecular Biology, Pennsylvania State University, University Park, United States
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Simon Gladman
53Melbourne Bioinformatics, University of Melbourne, Melbourne, Australia
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Saket Choudhary
54Computational Biology and Bioinformatics, University of Southern California, Los Angeles, United States
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Nicholas Harding
49Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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Florian Eggenhofer
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Arne Kratz
11Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
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Zhuoqing Fang
55Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai China
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Robert Kleinkauf
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Henning Timm
57Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Peter J. A. Cock
58The James Hutton Institute, Dundee, United Kingdom
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Enrico Seiler
39Bioinformatics Unit, Robert Koch Institute, Berlin, Germany
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Colin Brislawn
59Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, United States
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Hai Nguyen
60Department of Chemistry Chemical Biology, Rutgers University, Piscataway, United States
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Endre Bakken Stovner
61Department of Computer Science, Norwegian University of Science and Technology
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Philip Ewels
62Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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Matt Chambers
63Department of Biochemistry, Molecular Biology and Biophysics (as contractor, not employee), University of Minnesota, Minneapolis, United States
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James E. Johnson
64Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, United States
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Emil Hägglund
65Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
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Simon Ye
66Massachusetts Institute of Technology, Cambridge, United States
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Roman Valls Guimera
67Center for Cancer Research, University of Melbourne, Melbourne, Australia
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Elmar Pruesse
68University of Colorado, Denver, United States
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W. Augustine Dunn
69Boston Children’s Hospital, Boston, United States
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Lance Parsons
70Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
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Rob Patro
71Department of Computer Science, Stony Brook University, Stony Brook, United States
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David Koppstein
72The Kirby Institute of Infection and Immunity, University of New South Wales, Sydney, Australia
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Elena Grassi
73Transcription and Chromatin Lab, Humanitas University, Rozzano, Italy
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Inken Wohlers
74Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Integrative Experimental Genomics, University of Lübeck, Lübeck, Germany
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Alex Reynolds
75Altius Institute for Biomedical Sciences, Seattle, United States
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MacIntosh Cornwell
76New York University School of Medicine, New York City, United States
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Nicholas Stoler
77Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, United States
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Daniel Blankenberg
78Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
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Guowei He
79High Performance Computing, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
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Marcel Bargull
57Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Alexander Junge
80Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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Rick Farouni
81Massachusetts General Hospital and Harvard Medical School, Boston, United States
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Mallory Freeberg
82EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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Sourav Singh
83Savitribai Phule Pune University, Pune, Maharashtra, India
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Daniel R. Bogema
84NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
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Fabio Cumbo
85Department of Engineering, Roma Tre University, Rome, Italy
86Institute for Systems Analysis and Computer Science ”Antonio Ruberti”, National Research Council of Italy, Rome, Italy
77Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, United States
87SYSBIO.IT Center for Systems Biology, Milan, Italy
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Liang-Bo Wang
88Oncology Division, Department of Medicine, Washington University School of Medicine, St. Louis, United States
89McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States
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David E Larson
90The McDonnell Genome Institute, Washington University, St. Louis, United States
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Matthew L. Workentine
91Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
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Upendra Kumar Devisetty
92CyVerse, Bio5 institute, University of Arizona, Tucson, United States
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Sacha Laurent
93Institute of Microbiology, Universitary Hospital of Lausanne, Switzerland
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Pierrick Roger
94CEA, LIST, Laboratory for data analysis and systems’ intelligence, MetaboHUB, France
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Xavier Garnier
16INRA, UMR IGEPP, BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
95Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences, Inria/IRISA, Campus Beaulieu, Rennes, France
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Rasmus Agren
96Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Sweden
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Aziz Khan
97Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
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John M Eppley
98Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, United States
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Wei Li
99Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, United States
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Bianca Katharina Stöcker
57Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Tobias Rausch
100European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany
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James Taylor
101Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, United States
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Patrick R. Wright
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Adam P. Taranto
102Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, Australia
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Davide Chicco
103Princess Margaret Cancer Centre, Toronto, Canada
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Bengt Sennblad
26Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Jasmijn A. Baaijens
104Centrum Wiskunde and Informatica, Amsterdam, Netherlands
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Matthew Gopez
42National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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Nezar Abdennur
66Massachusetts Institute of Technology, Cambridge, United States
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Iain Milne
58The James Hutton Institute, Dundee, United Kingdom
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Jens Preussner
105ECCPS Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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81Massachusetts General Hospital and Harvard Medical School, Boston, United States
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71Department of Computer Science, Stony Brook University, Stony Brook, United States
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106Applied Bioinformatics Laboratory, 2 Ravinia Drive, Suite 1200 Atlanta, GA 30346, United States
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107German Cancer Research Center (DKFZ), Foundation under Public Law, Heidelberg, Germany
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108Dip. di Informatica Sistemistica e Comunicazione, Univ. degli Studi di Milano-Bicocca, Milan, Italy
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109Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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110Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, United States
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111The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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112ZBH - Center for Bioinformatics, MIN-Fakultät, Universität Hamburg, Hamburg, Germany
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8Broad Institute of MIT and Harvard, Cambridge, United States
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113Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
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Nicholas R. Waters
114Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland
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Saskia Hiltemann
115Erasmus Medical Center, Rotterdam, The Netherlands
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Matthew L. Bendall
116Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, D.C., United States
117Department of Microbiology, Immunology Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C., United States
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Christoph Stahl
118Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg Essen, Essen, Germany
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Alistair Miles
49Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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Yannick Boursin
119Institut Gustave Roussy, Villejuif, France
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Yasset Perez-Riverol
120European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Sebastian Schmeier
121Massey University, Institute of Natural and Mathematical Sciences, North Shore City, New Zealand
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Erik Clarke
122Department of Microbiology, University of Pennsylvania, United States
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123GeneDx, Gaithersburg, United States
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124Institut de G´en´etique et de Biologie Mol´eculaire et Cellulaire, CNRS, Illkirch, France
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125Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom
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124Institut de G´en´etique et de Biologie Mol´eculaire et Cellulaire, CNRS, Illkirch, France
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1Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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126Epigenetic Regulation Unit, Pasteur Institute, Paris, France
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127Biodiversity, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
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128Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
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Alexander S Mikheyev
129Evolutionary Genomics Lab, Research School of Biology, The Australian National University, Canberra, Australia
130Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Kunigami-gun, Okinawa, Japan
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42National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
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131Universitat Rovira i Virgili, Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Reus Spain
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Christopher Schröder
132Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany
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Adrian Emanuel Salatino
133Department of Molecular Genetics and Biology of Complex Diseases, Institute of Medical Research A Lanari-IDIM, University of Buenos Aires, National Scientific and Technical Research Council (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.
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Simon Dirmeier
134Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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Timothy H. Webster
135School of Life Sciences, Arizona State University, Tempe, United States
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Oleksandr Moskalenko
136UFIT Research Computing, University of Florida, Gainesville, United States
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Gordon Stephen
58The James Hutton Institute, Dundee, United Kingdom
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Johannes Köster
137Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen
138Dana Farber Cancer Institute, Harvard Medical School, Boston, United States October 27, 2017
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Abstract

We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.

Footnotes

  • ↵∗ Co-first author

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S Pedersen, Youri Hoogstrate, Anthony Bretaudeau, Devon Ryan, Gildas Le Corguillé, Dilmurat Yusuf, Sebastian Luna-Valero, Rory Kirchner, Karel Brinda, Thomas Wollmann, Martin Raden, Simon J. van Heeringen, Nicola Soranzo, Lorena Pantano, Zachary Charlop-Powers, Per Unneberg, Matthias De Smet, Marcel Martin, Greg Von Kuster, Tiago Antao, Milad Miladi, Kevin Thornton, Christian Brueffer, Marius van den Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, K´evin Gravouil, Joachim Wolff, Manuel Holtgrewe, Jörg Fallmann, Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif, Philip Mabon, Xiao-Ou Zhang, Wei Shen, Jennifer Cabral, Cristel Thomas, Eric Enns, Joseph Brown, Jorrit Boekel, Mattias de Hollander, Jerome Kelleher, Nitesh Turaga, Julian R. de Ruiter, Dave Bouvier, Simon Gladman, Saket Choudhary, Nicholas Harding, Florian Eggenhofer, Arne Kratz, Zhuoqing Fang, Robert Kleinkauf, Henning Timm, Peter J. A. Cock, Enrico Seiler, Colin Brislawn, Hai Nguyen, Endre Bakken Stovner, Philip Ewels, Matt Chambers, James E. Johnson, Emil Hägglund, Simon Ye, Roman Valls Guimera, Elmar Pruesse, W. Augustine Dunn, Lance Parsons, Rob Patro, David Koppstein, Elena Grassi, Inken Wohlers, Alex Reynolds, MacIntosh Cornwell, Nicholas Stoler, Daniel Blankenberg, Guowei He, Marcel Bargull, Alexander Junge, Rick Farouni, Mallory Freeberg, Sourav Singh, Daniel R. Bogema, Fabio Cumbo, Liang-Bo Wang, David E Larson, Matthew L. Workentine, Upendra Kumar Devisetty, Sacha Laurent, Pierrick Roger, Xavier Garnier, Rasmus Agren, Aziz Khan, John M Eppley, Wei Li, Bianca Katharina Stöcker, Tobias Rausch, James Taylor, Patrick R. Wright, Adam P. Taranto, Davide Chicco, Bengt Sennblad, Jasmijn A. Baaijens, Matthew Gopez, Nezar Abdennur, Iain Milne, Jens Preussner, Luca Pinello, Avi Srivastava, Aroon T. Chande, Philip Reiner Kensche, Yuri Pirola, Michael Knudsen, Ino de Bruijn, Kai Blin, Giorgio Gonnella, Oana M. Enache, Vivek Rai, Nicholas R. Waters, Saskia Hiltemann, Matthew L. Bendall, Christoph Stahl, Alistair Miles, Yannick Boursin, Yasset Perez-Riverol, Sebastian Schmeier, Erik Clarke, Kevin Arvai, Matthieu Jung, Tom´as Di Domenico, Julien Seiler, Eric Rasche, Etienne Kornobis, Daniela Beisser, Sven Rahmann, Alexander S Mikheyev, Camy Tran, Jordi Capellades, Christopher Schröder, Adrian Emanuel Salatino, Simon Dirmeier, Timothy H. Webster, Oleksandr Moskalenko, Gordon Stephen, Johannes Köster
bioRxiv 207092; doi: https://doi.org/10.1101/207092
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S Pedersen, Youri Hoogstrate, Anthony Bretaudeau, Devon Ryan, Gildas Le Corguillé, Dilmurat Yusuf, Sebastian Luna-Valero, Rory Kirchner, Karel Brinda, Thomas Wollmann, Martin Raden, Simon J. van Heeringen, Nicola Soranzo, Lorena Pantano, Zachary Charlop-Powers, Per Unneberg, Matthias De Smet, Marcel Martin, Greg Von Kuster, Tiago Antao, Milad Miladi, Kevin Thornton, Christian Brueffer, Marius van den Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, K´evin Gravouil, Joachim Wolff, Manuel Holtgrewe, Jörg Fallmann, Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif, Philip Mabon, Xiao-Ou Zhang, Wei Shen, Jennifer Cabral, Cristel Thomas, Eric Enns, Joseph Brown, Jorrit Boekel, Mattias de Hollander, Jerome Kelleher, Nitesh Turaga, Julian R. de Ruiter, Dave Bouvier, Simon Gladman, Saket Choudhary, Nicholas Harding, Florian Eggenhofer, Arne Kratz, Zhuoqing Fang, Robert Kleinkauf, Henning Timm, Peter J. A. Cock, Enrico Seiler, Colin Brislawn, Hai Nguyen, Endre Bakken Stovner, Philip Ewels, Matt Chambers, James E. Johnson, Emil Hägglund, Simon Ye, Roman Valls Guimera, Elmar Pruesse, W. Augustine Dunn, Lance Parsons, Rob Patro, David Koppstein, Elena Grassi, Inken Wohlers, Alex Reynolds, MacIntosh Cornwell, Nicholas Stoler, Daniel Blankenberg, Guowei He, Marcel Bargull, Alexander Junge, Rick Farouni, Mallory Freeberg, Sourav Singh, Daniel R. Bogema, Fabio Cumbo, Liang-Bo Wang, David E Larson, Matthew L. Workentine, Upendra Kumar Devisetty, Sacha Laurent, Pierrick Roger, Xavier Garnier, Rasmus Agren, Aziz Khan, John M Eppley, Wei Li, Bianca Katharina Stöcker, Tobias Rausch, James Taylor, Patrick R. Wright, Adam P. Taranto, Davide Chicco, Bengt Sennblad, Jasmijn A. Baaijens, Matthew Gopez, Nezar Abdennur, Iain Milne, Jens Preussner, Luca Pinello, Avi Srivastava, Aroon T. Chande, Philip Reiner Kensche, Yuri Pirola, Michael Knudsen, Ino de Bruijn, Kai Blin, Giorgio Gonnella, Oana M. Enache, Vivek Rai, Nicholas R. Waters, Saskia Hiltemann, Matthew L. Bendall, Christoph Stahl, Alistair Miles, Yannick Boursin, Yasset Perez-Riverol, Sebastian Schmeier, Erik Clarke, Kevin Arvai, Matthieu Jung, Tom´as Di Domenico, Julien Seiler, Eric Rasche, Etienne Kornobis, Daniela Beisser, Sven Rahmann, Alexander S Mikheyev, Camy Tran, Jordi Capellades, Christopher Schröder, Adrian Emanuel Salatino, Simon Dirmeier, Timothy H. Webster, Oleksandr Moskalenko, Gordon Stephen, Johannes Köster
bioRxiv 207092; doi: https://doi.org/10.1101/207092

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