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