New Results
Bioconda: A sustainable and comprehensive software distribution for the life sciences
Ryan Dale, Björn Grüning, Andreas Sjödin, Jillian Rowe, Brad A. Chapman, Christopher H. Tomkins-Tinch, Renan Valieris, Bérénice Batut, Adam Caprez, Thomas Cokelaer, Dilmurat Yusuf, Kyle A. Beauchamp, Karel Brinda, Thomas Wollmann, Gildas Le Corguillé, Devon Ryan, Anthony Bretaudeau, Youri Hoogstrate, Brent S Pedersen, Simon van Heeringen, Martin Raden, Sebastian Luna-Valero, Nicola Soranzo, Matthias De Smet, Greg Von Kuster, Rory Kirchner, Lorena Pantano, Zachary Charlop-Powers, Kevin Thornton, Marcel Martin, Marius van den Beek, Daniel Maticzka, Milad Miladi, Sebastian Will, Kévin Gravouil, Per Unneberg, Christian Brueffer, Clemens Blank, Vitor C. Piro, Joachim Wolff, Tiago Antao, Simon Gladman, Ilya Shlyakhter, Mattias de Hollander, Philip Mabon, Wei Shen, Jorrit Boekel, Manuel Holtgrewe, Dave Bouvier, Julian R. de Ruiter, Jennifer Cabral, Saket Choudhary, Nicholas Harding, Robert Kleinkauf, Eric Enns, Florian Eggenhofer, Joseph Brown, Peter J. A. Cock, Henning Timm, Cristel Thomas, Xiao-Ou Zhang, Matt Chambers, Nitesh Turaga, Enrico Seiler, Colin Brislawn, Elmar Pruesse, Jörg Fallmann, Jerome Kelleher, Hai Nguyen, Lance Parsons, Zhuoqing Fang, Endre Bakken Stovner, Nicholas Stoler, Simon Ye, Inken Wohlers, Rick Farouni, Mallory Freeberg, James E. Johnson, Marcel Bargull, Philip Reiner Kensche, Timothy H. Webster, John M Eppley, Christoph Stahl, Alexander S. Rose, Alex Reynolds, Liang-Bo Wang, Xavier Garnier, Simon Dirmeier, Michael Knudsen, James Taylor, Avi Srivastava, Vivek Rai, Rasmus Agren, Alexander Junge, Roman Valls Guimera, Aziz Khan, Sebastian Schmeier, Guowei He, Luca Pinello, Emil Hägglund, Alexander S. Mikheyev, Jens Preussner, Nicholas R. Waters, Wei Li, Jordi Capellades, Aroon T. Chande, Yuri Pirola, Saskia Hiltemann, Matthew L. Bendall, Sourav Singh, W. Augustine Dunn, Alexandre Drouin, Tomás Di Domenico, Ino de Bruijn, David E. Larson, Davide Chicco, Elena Grassi, Giorgio Gonnella, B. Jaivarsan, Liya Wang, Franck Giacomoni, Erik Clarke, Daniel Blankenberg, Camy Tran, Rob Patro, Sacha Laurent, Matthew Gopez, Bengt Sennblad, Jasmijn A. Baaijens, Philip Ewels, Patrick R. Wright, Oana M. Enache, Pierrick Roger, Will Dampier, David Koppstein, Upendra Kumar Devisetty, Tobias Rausch, MacIntosh Cornwell, Adrian Emanuel Salatino, Julien Seiler, Matthieu Jung, Etienne Kornobis, Fabio Cumbo, Bianca Katharina Stöcker, Oleksandr Moskalenko, Daniel R. Bogema, Matthew L. Workentine, Stephen J. Newhouse, Felipe da Veiga Leprevost, Kevin Arvai, Johannes Köster
doi: https://doi.org/10.1101/207092
Ryan Dale
1Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
Björn Grüning
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Andreas Sjödin
3Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå. Sweden
4Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå Sweden
Jillian Rowe
5NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
Brad A. Chapman
6Harvard T.H. Chan School of Public Health, Boston, United States
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, São Paulo, Brazil
Bérénice Batut
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Adam Caprez
10Holland Computing Center, University of Nebraska, Lincoln, United States
Thomas Cokelaer
11Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, Paris, France
Dilmurat Yusuf
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Kyle A. Beauchamp
12Counsyl, South San Francisco, United States
Karel Brinda
13Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States
Thomas Wollmann
14University of Heidelberg and DKFZ, Heidelberg, Germany
Gildas Le Corguillé
15UPMC, CNRS, FR2424, ABiMS, Station Biologique Roscoff, France
Devon Ryan
16Bioinformatics core facility, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
Anthony Bretaudeau
17INRA, UMR IGEPP, BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
Youri Hoogstrate
18Erasmus Medical Center, Department of Urology, Rotterdam, The Netherlands
Brent S Pedersen
19Department of Human Genetics, University of Utah, Eccles Institute of Human Genetics, Salt Lake City
Simon van Heeringen
20Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
Martin Raden
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Sebastian Luna-Valero
21MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
Nicola Soranzo
22Earlham Institute, Norwich Research Park, Norwich, United Kindgom
Matthias De Smet
23Ghent University Hospital, Ghent University, Belgium
Greg Von Kuster
24Institute for CyberScience, Penn State University, University Park, United States
Rory Kirchner
25Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States
Lorena Pantano
6Harvard T.H. Chan School of Public Health, Boston, United States
Zachary Charlop-Powers
26The Laboratory for Genetically Encoded Small Molecules, The Rockefeller University, New York, United States
Kevin Thornton
27Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, United States
Marcel Martin
28Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Sweden
Marius van den Beek
29Stem Cells and Tissue Homeostasis, Institut Curie, Paris, France
Daniel Maticzka
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Milad Miladi
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Sebastian Will
30Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
Kévin Gravouil
31Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
Per Unneberg
32Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Christian Brueffer
33Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
Clemens Blank
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Vitor C. Piro
34Bioinformatics Unit, Robert Koch Institute, Berlin, Germany
35CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
Joachim Wolff
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Tiago Antao
36Division of Biological Sciences, University of Montana, Missoula, United States of America
Simon Gladman
37Melbourne Bioinformatics, University of Melbourne, Melbourne, Australia
Ilya Shlyakhter
8Broad Institute of MIT and Harvard, Cambridge, United States
Mattias de Hollander
38Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
Philip Mabon
39National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Wei Shen
40Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu, China
Jorrit Boekel
41Department of Oncology-Pathology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
Manuel Holtgrewe
42Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
43Charité Universitätsmedizin Berlin, Berlin, Germany
Dave Bouvier
44Department of Biochemistry Molecular Biology, Penn State University, University Park, United States
Julian R. de Ruiter
45Divisions of Molecular Pathology and Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
Jennifer Cabral
39National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Saket Choudhary
46Computational Biology and Bioinformatics, University of Southern California, Los Angeles, United States
Nicholas Harding
47Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
Robert Kleinkauf
48Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
Eric Enns
39National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Florian Eggenhofer
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Joseph Brown
49Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
Peter J. A. Cock
50The James Hutton Institute, Dundee, United Kingdom
Henning Timm
51Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Cristel Thomas
52Northrop Grumman Corporation, Technology Services, Rockville, United States
Xiao-Ou Zhang
53Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
Matt Chambers
54Department of Biochemistry, Molecular Biology and Biophysics (as contractor, not employee), University of Minnesota, Minneapolis, United States
Nitesh Turaga
55Department of Biology, Johns Hopkins University, Baltimore, United States
Enrico Seiler
34Bioinformatics Unit, Robert Koch Institute, Berlin, Germany
Colin Brislawn
56Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, United States
Elmar Pruesse
57University of Colorado, Denver, United States
Jörg Fallmann
58Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
Jerome Kelleher
47Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
Hai Nguyen
59Department of Chemistry Chemical Biology, Rutgers University, Piscataway, United States
Lance Parsons
60Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
Zhuoqing Fang
61Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai China
Endre Bakken Stovner
62Department of Computer Science, Norwegian University of Science and Technology
Nicholas Stoler
63Department of Biochemistry and Molecular Biology, Penn State University, University Park, United States
Simon Ye
64Massachusetts Institute of Technology, Cambridge, United States
Inken Wohlers
65Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Integrative Experimental Genomics, University of Lüubeck, Lüubeck, Germany
Rick Farouni
66Massachusetts General Hospital and Harvard Medical School, Boston, United States
Mallory Freeberg
67EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
James E. Johnson
68Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, United States
Marcel Bargull
51Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Philip Reiner Kensche
69German Cancer Research Center (DKFZ), Foundation under Public Law, Heidelberg, Germany
Timothy H. Webster
70School of Life Sciences, Arizona State University, Tempe, United States
John M Eppley
71Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, United States
Christoph Stahl
72Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg Essen, Essen, Germany
Alexander S. Rose
73RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, United States
Alex Reynolds
74Altius Institute for Biomedical Sciences, Seattle, United States
Liang-Bo Wang
75Oncology Division, Department of Medicine, Washington University School of Medicine, St. Louis, United States
76McDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States
Xavier Garnier
17INRA, UMR IGEPP, BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
77Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences, Inria/IRISA, Campus Beaulieu, Rennes, France
Simon Dirmeier
78Department of Biosystems Science and Engineering,ETH Zurich, Basel, Switzerland
Michael Knudsen
79Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
James Taylor
80Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, United States
Avi Srivastava
81Department of Computer Science, Stony Brook University, Stony Brook, United States
Vivek Rai
82Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
Rasmus Agren
83Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Sweden
Alexander Junge
84Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
Roman Valls Guimera
85Center for Cancer Research, University of Melbourne, Melbourne, Australia
Aziz Khan
86Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
Sebastian Schmeier
87Massey University, Institute of Natural and Mathematical Sciences, North Shore City, New Zealand
Guowei He
88High Performance Computing, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
Luca Pinello
66Massachusetts General Hospital and Harvard Medical School, Boston, United States
Emil Hägglund
89Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
Alexander S. Mikheyev
90Evolutionary Genomics Lab, Research School of Biology, The Australian National University, Canberra, Australia
91Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Kunigami-gun, Okinawa, Japan
Jens Preussner
92ECCPS Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
Nicholas R. Waters
93Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland
Wei Li
94Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, United States
Jordi Capellades
95Universitat Rovira i Virgili, Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Reus Spain
Aroon T. Chande
96Applied Bioinformatics Laboratory, 2 Ravinia Drive, Suite 1200 Atlanta, GA 30346, United States
Yuri Pirola
97Dip. di Informatica Sistemistica e Comunicazione, Univ. degli Studi di Milano-Bicocca, Milan, Italy
Saskia Hiltemann
98Erasmus Medical Center, Rotterdam, The Netherlands
Matthew L. Bendall
99Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, D.C., United States
100Department of Microbiology, Immunology Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C., United States
Sourav Singh
101Savitribai Phule Pune University, Pune, Maharashtra, India
W. Augustine Dunn
102Boston Children’s Hospital, Boston, United States
Alexandre Drouin
103Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
Tomás Di Domenico
104Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom
Ino de Bruijn
105Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, United States
David E. Larson
106The McDonnell Genome Institute, Washington University, St. Louis, United States
Davide Chicco
107Princess Margaret Cancer Centre, Toronto, Canada
Elena Grassi
108Transcription and Chromatin Lab, Humanitas University, Rozzano, Italy
Giorgio Gonnella
109ZBH-Center for Bioinformatics, MIN-Fakultät, Universität Hamburg, Hamburg, Germany
B. Jaivarsan
110Department of Computer Science, Computer science with specialisation in Bioinformatics, VIT University Vellore, India
Liya Wang
111Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
Franck Giacomoni
112Clermont Auvergne University,INRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont-Ferrand, France
Erik Clarke
113Department of Microbiology, University of Pennsylvania, United States
Daniel Blankenberg
114Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
Camy Tran
39National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Rob Patro
81Department of Computer Science, Stony Brook University, Stony Brook, United States
Sacha Laurent
115Institute of Microbiology, Universitary Hospital of Lausanne, Switzerland
Matthew Gopez
39National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Bengt Sennblad
32Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Jasmijn A. Baaijens
116Centrum Wiskunde and Informatica, Amsterdam, Netherlands
Philip Ewels
117Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
Patrick R. Wright
2Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Oana M. Enache
8Broad Institute of MIT and Harvard, Cambridge, United States
Pierrick Roger
118CEA, LIST, Laboratory for data analysis and systems’ intelligence, MetaboHUB, France
Will Dampier
119Drexel University College of Medicine, Department of Microbiology and Immunology, Philadelphia, United States
David Koppstein
120The Kirby Institute of Infection and Immunity, University of New South Wales, Sydney, Australia
Upendra Kumar Devisetty
121CyVerse, Bio5 institute, University of Arizona, Tucson, United States
Tobias Rausch
122European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany
MacIntosh Cornwell
123New York University School of Medicine, New York City, United States
Adrian Emanuel Salatino
124Department 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.
Julien Seiler
125Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, Illkirch, France
Matthieu Jung
125Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, Illkirch, France
Etienne Kornobis
126Epigenetic Regulation Unit, Pasteur Institute, Paris, France
Fabio Cumbo
127Department of Engineering, Roma Tre University, Rome, Italy
128Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council of Italy, Rome, Italy
63Department of Biochemistry and Molecular Biology, Penn State University, University Park, United States
Bianca Katharina Stöcker
51Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Oleksandr Moskalenko
129UFIT Research Computing, University of Florida, Gainesville, United States
Daniel R. Bogema
130NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
Matthew L. Workentine
131Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
Stephen J. Newhouse
132Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
133NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, United Kingdom
134Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, United Kingdom
Felipe da Veiga Leprevost
135Pathology Department, University of Michigan, Ann Arbor, United States
Kevin Arvai
136GeneDx, Gaithersburg, United States
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
Abstract
We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager, Conda. Currently, Bioconda offers a collection of over 2900 software tools, which are 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.
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 21, 2017.
Bioconda: A sustainable and comprehensive software distribution for the life sciences
Ryan Dale, Björn Grüning, Andreas Sjödin, Jillian Rowe, Brad A. Chapman, Christopher H. Tomkins-Tinch, Renan Valieris, Bérénice Batut, Adam Caprez, Thomas Cokelaer, Dilmurat Yusuf, Kyle A. Beauchamp, Karel Brinda, Thomas Wollmann, Gildas Le Corguillé, Devon Ryan, Anthony Bretaudeau, Youri Hoogstrate, Brent S Pedersen, Simon van Heeringen, Martin Raden, Sebastian Luna-Valero, Nicola Soranzo, Matthias De Smet, Greg Von Kuster, Rory Kirchner, Lorena Pantano, Zachary Charlop-Powers, Kevin Thornton, Marcel Martin, Marius van den Beek, Daniel Maticzka, Milad Miladi, Sebastian Will, Kévin Gravouil, Per Unneberg, Christian Brueffer, Clemens Blank, Vitor C. Piro, Joachim Wolff, Tiago Antao, Simon Gladman, Ilya Shlyakhter, Mattias de Hollander, Philip Mabon, Wei Shen, Jorrit Boekel, Manuel Holtgrewe, Dave Bouvier, Julian R. de Ruiter, Jennifer Cabral, Saket Choudhary, Nicholas Harding, Robert Kleinkauf, Eric Enns, Florian Eggenhofer, Joseph Brown, Peter J. A. Cock, Henning Timm, Cristel Thomas, Xiao-Ou Zhang, Matt Chambers, Nitesh Turaga, Enrico Seiler, Colin Brislawn, Elmar Pruesse, Jörg Fallmann, Jerome Kelleher, Hai Nguyen, Lance Parsons, Zhuoqing Fang, Endre Bakken Stovner, Nicholas Stoler, Simon Ye, Inken Wohlers, Rick Farouni, Mallory Freeberg, James E. Johnson, Marcel Bargull, Philip Reiner Kensche, Timothy H. Webster, John M Eppley, Christoph Stahl, Alexander S. Rose, Alex Reynolds, Liang-Bo Wang, Xavier Garnier, Simon Dirmeier, Michael Knudsen, James Taylor, Avi Srivastava, Vivek Rai, Rasmus Agren, Alexander Junge, Roman Valls Guimera, Aziz Khan, Sebastian Schmeier, Guowei He, Luca Pinello, Emil Hägglund, Alexander S. Mikheyev, Jens Preussner, Nicholas R. Waters, Wei Li, Jordi Capellades, Aroon T. Chande, Yuri Pirola, Saskia Hiltemann, Matthew L. Bendall, Sourav Singh, W. Augustine Dunn, Alexandre Drouin, Tomás Di Domenico, Ino de Bruijn, David E. Larson, Davide Chicco, Elena Grassi, Giorgio Gonnella, B. Jaivarsan, Liya Wang, Franck Giacomoni, Erik Clarke, Daniel Blankenberg, Camy Tran, Rob Patro, Sacha Laurent, Matthew Gopez, Bengt Sennblad, Jasmijn A. Baaijens, Philip Ewels, Patrick R. Wright, Oana M. Enache, Pierrick Roger, Will Dampier, David Koppstein, Upendra Kumar Devisetty, Tobias Rausch, MacIntosh Cornwell, Adrian Emanuel Salatino, Julien Seiler, Matthieu Jung, Etienne Kornobis, Fabio Cumbo, Bianca Katharina Stöcker, Oleksandr Moskalenko, Daniel R. Bogema, Matthew L. Workentine, Stephen J. Newhouse, Felipe da Veiga Leprevost, Kevin Arvai, Johannes Köster
bioRxiv 207092; doi: https://doi.org/10.1101/207092
Bioconda: A sustainable and comprehensive software distribution for the life sciences
Ryan Dale, Björn Grüning, Andreas Sjödin, Jillian Rowe, Brad A. Chapman, Christopher H. Tomkins-Tinch, Renan Valieris, Bérénice Batut, Adam Caprez, Thomas Cokelaer, Dilmurat Yusuf, Kyle A. Beauchamp, Karel Brinda, Thomas Wollmann, Gildas Le Corguillé, Devon Ryan, Anthony Bretaudeau, Youri Hoogstrate, Brent S Pedersen, Simon van Heeringen, Martin Raden, Sebastian Luna-Valero, Nicola Soranzo, Matthias De Smet, Greg Von Kuster, Rory Kirchner, Lorena Pantano, Zachary Charlop-Powers, Kevin Thornton, Marcel Martin, Marius van den Beek, Daniel Maticzka, Milad Miladi, Sebastian Will, Kévin Gravouil, Per Unneberg, Christian Brueffer, Clemens Blank, Vitor C. Piro, Joachim Wolff, Tiago Antao, Simon Gladman, Ilya Shlyakhter, Mattias de Hollander, Philip Mabon, Wei Shen, Jorrit Boekel, Manuel Holtgrewe, Dave Bouvier, Julian R. de Ruiter, Jennifer Cabral, Saket Choudhary, Nicholas Harding, Robert Kleinkauf, Eric Enns, Florian Eggenhofer, Joseph Brown, Peter J. A. Cock, Henning Timm, Cristel Thomas, Xiao-Ou Zhang, Matt Chambers, Nitesh Turaga, Enrico Seiler, Colin Brislawn, Elmar Pruesse, Jörg Fallmann, Jerome Kelleher, Hai Nguyen, Lance Parsons, Zhuoqing Fang, Endre Bakken Stovner, Nicholas Stoler, Simon Ye, Inken Wohlers, Rick Farouni, Mallory Freeberg, James E. Johnson, Marcel Bargull, Philip Reiner Kensche, Timothy H. Webster, John M Eppley, Christoph Stahl, Alexander S. Rose, Alex Reynolds, Liang-Bo Wang, Xavier Garnier, Simon Dirmeier, Michael Knudsen, James Taylor, Avi Srivastava, Vivek Rai, Rasmus Agren, Alexander Junge, Roman Valls Guimera, Aziz Khan, Sebastian Schmeier, Guowei He, Luca Pinello, Emil Hägglund, Alexander S. Mikheyev, Jens Preussner, Nicholas R. Waters, Wei Li, Jordi Capellades, Aroon T. Chande, Yuri Pirola, Saskia Hiltemann, Matthew L. Bendall, Sourav Singh, W. Augustine Dunn, Alexandre Drouin, Tomás Di Domenico, Ino de Bruijn, David E. Larson, Davide Chicco, Elena Grassi, Giorgio Gonnella, B. Jaivarsan, Liya Wang, Franck Giacomoni, Erik Clarke, Daniel Blankenberg, Camy Tran, Rob Patro, Sacha Laurent, Matthew Gopez, Bengt Sennblad, Jasmijn A. Baaijens, Philip Ewels, Patrick R. Wright, Oana M. Enache, Pierrick Roger, Will Dampier, David Koppstein, Upendra Kumar Devisetty, Tobias Rausch, MacIntosh Cornwell, Adrian Emanuel Salatino, Julien Seiler, Matthieu Jung, Etienne Kornobis, Fabio Cumbo, Bianca Katharina Stöcker, Oleksandr Moskalenko, Daniel R. Bogema, Matthew L. Workentine, Stephen J. Newhouse, Felipe da Veiga Leprevost, Kevin Arvai, Johannes Köster
bioRxiv 207092; doi: https://doi.org/10.1101/207092
Subject Area
Subject Areas
- Biochemistry (4355)
- Bioengineering (3003)
- Bioinformatics (13602)
- Biophysics (6045)
- Cancer Biology (4705)
- Cell Biology (6718)
- Clinical Trials (138)
- Developmental Biology (3979)
- Ecology (6297)
- Epidemiology (2054)
- Evolutionary Biology (9277)
- Genetics (6942)
- Genomics (8903)
- Immunology (3990)
- Microbiology (11452)
- Molecular Biology (4515)
- Neuroscience (25983)
- Paleontology (184)
- Pathology (734)
- Pharmacology and Toxicology (1230)
- Physiology (1805)
- Plant Biology (4049)
- Synthetic Biology (1205)
- Systems Biology (3664)
- Zoology (665)