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
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
Björn Grüning
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Andreas Sjödin
Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå. SwedenDepartment of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå Sweden
Jillian Rowe
NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
Brad A. Chapman
Harvard T.H. Chan School of Public Health, Boston, United States
Christopher H. Tomkins-Tinch
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United States
Renan Valieris
Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, São Paulo, Brazil
Bérénice Batut
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Adam Caprez
Holland Computing Center, University of Nebraska, Lincoln, United States
Thomas Cokelaer
Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, Paris, France
Dilmurat Yusuf
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Kyle A. Beauchamp
Counsyl, South San Francisco, United States
Karel Brinda
Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States
Thomas Wollmann
University of Heidelberg and DKFZ, Heidelberg, Germany
Gildas Le Corguillé
UPMC, CNRS, FR2424, ABiMS, Station Biologique Roscoff, France
Devon Ryan
Bioinformatics core facility, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
Anthony Bretaudeau
INRA, UMR IGEPP, BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
Youri Hoogstrate
Erasmus Medical Center, Department of Urology, Rotterdam, The Netherlands
Brent S Pedersen
Department of Human Genetics, University of Utah, Eccles Institute of Human Genetics, Salt Lake City
Simon van Heeringen
Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
Martin Raden
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Sebastian Luna-Valero
MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
Nicola Soranzo
Earlham Institute, Norwich Research Park, Norwich, United Kindgom
Matthias De Smet
Ghent University Hospital, Ghent University, Belgium
Greg Von Kuster
Institute for CyberScience, Penn State University, University Park, United States
Rory Kirchner
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States
Lorena Pantano
Harvard T.H. Chan School of Public Health, Boston, United States
Zachary Charlop-Powers
The Laboratory for Genetically Encoded Small Molecules, The Rockefeller University, New York, United States
Kevin Thornton
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, United States
Marcel Martin
Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Sweden
Marius van den Beek
Stem Cells and Tissue Homeostasis, Institut Curie, Paris, France
Daniel Maticzka
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Milad Miladi
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Sebastian Will
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
Kévin Gravouil
Université Clermont Auvergne, INRA, MEDIS, Clermont-Ferrand, France
Per Unneberg
Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Christian Brueffer
Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
Clemens Blank
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Vitor C. Piro
Bioinformatics Unit, Robert Koch Institute, Berlin, GermanyCAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
Joachim Wolff
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Tiago Antao
Division of Biological Sciences, University of Montana, Missoula, United States of America
Simon Gladman
Melbourne Bioinformatics, University of Melbourne, Melbourne, Australia
Ilya Shlyakhter
Broad Institute of MIT and Harvard, Cambridge, United States
Mattias de Hollander
Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
Philip Mabon
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Wei Shen
Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu, China
Jorrit Boekel
Department of Oncology-Pathology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
Manuel Holtgrewe
Core Unit Bioinformatics, Berlin Institute of Health, Berlin, GermanyCharité Universitätsmedizin Berlin, Berlin, Germany
Dave Bouvier
Department of Biochemistry Molecular Biology, Penn State University, University Park, United States
Julian R. de Ruiter
Divisions of Molecular Pathology and Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
Jennifer Cabral
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Saket Choudhary
Computational Biology and Bioinformatics, University of Southern California, Los Angeles, United States
Nicholas Harding
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
Robert Kleinkauf
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
Eric Enns
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Florian Eggenhofer
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Joseph Brown
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, United States
Peter J. A. Cock
The James Hutton Institute, Dundee, United Kingdom
Henning Timm
Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Cristel Thomas
Northrop Grumman Corporation, Technology Services, Rockville, United States
Xiao-Ou Zhang
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
Matt Chambers
Department of Biochemistry, Molecular Biology and Biophysics (as contractor, not employee), University of Minnesota, Minneapolis, United States
Nitesh Turaga
Department of Biology, Johns Hopkins University, Baltimore, United States
Enrico Seiler
Bioinformatics Unit, Robert Koch Institute, Berlin, Germany
Colin Brislawn
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, United States
Elmar Pruesse
University of Colorado, Denver, United States
Jörg Fallmann
Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
Jerome Kelleher
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
Hai Nguyen
Department of Chemistry Chemical Biology, Rutgers University, Piscataway, United States
Lance Parsons
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
Zhuoqing Fang
Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai China
Endre Bakken Stovner
Department of Computer Science, Norwegian University of Science and Technology
Nicholas Stoler
Department of Biochemistry and Molecular Biology, Penn State University, University Park, United States
Simon Ye
Massachusetts Institute of Technology, Cambridge, United States
Inken Wohlers
Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), Institutes of Neurogenetics and Integrative Experimental Genomics, University of Lüubeck, Lüubeck, Germany
Rick Farouni
Massachusetts General Hospital and Harvard Medical School, Boston, United States
Mallory Freeberg
EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
James E. Johnson
Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, United States
Marcel Bargull
Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Philip Reiner Kensche
German Cancer Research Center (DKFZ), Foundation under Public Law, Heidelberg, Germany
Timothy H. Webster
School of Life Sciences, Arizona State University, Tempe, United States
John M Eppley
Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawaii, Honolulu, United States
Christoph Stahl
Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg Essen, Essen, Germany
Alexander S. Rose
RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, United States
Alex Reynolds
Altius Institute for Biomedical Sciences, Seattle, United States
Liang-Bo Wang
Oncology Division, Department of Medicine, Washington University School of Medicine, St. Louis, United StatesMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States
Xavier Garnier
INRA, UMR IGEPP, BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, FranceDyliss - Dynamics, Logics and Inference for biological Systems and Sequences, Inria/IRISA, Campus Beaulieu, Rennes, France
Simon Dirmeier
Department of Biosystems Science and Engineering,ETH Zurich, Basel, Switzerland
Michael Knudsen
Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
James Taylor
Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, United States
Avi Srivastava
Department of Computer Science, Stony Brook University, Stony Brook, United States
Vivek Rai
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
Rasmus Agren
Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Sweden
Alexander Junge
Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
Roman Valls Guimera
Center for Cancer Research, University of Melbourne, Melbourne, Australia
Aziz Khan
Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
Sebastian Schmeier
Massey University, Institute of Natural and Mathematical Sciences, North Shore City, New Zealand
Guowei He
High Performance Computing, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
Luca Pinello
Massachusetts General Hospital and Harvard Medical School, Boston, United States
Emil Hägglund
Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
Alexander S. Mikheyev
Evolutionary Genomics Lab, Research School of Biology, The Australian National University, Canberra, AustraliaEcology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Kunigami-gun, Okinawa, Japan
Jens Preussner
ECCPS Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
Nicholas R. Waters
Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland
Wei Li
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, United States
Jordi Capellades
Universitat Rovira i Virgili, Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Reus Spain
Aroon T. Chande
Applied Bioinformatics Laboratory, 2 Ravinia Drive, Suite 1200 Atlanta, GA 30346, United States
Yuri Pirola
Dip. di Informatica Sistemistica e Comunicazione, Univ. degli Studi di Milano-Bicocca, Milan, Italy
Saskia Hiltemann
Erasmus Medical Center, Rotterdam, The Netherlands
Matthew L. Bendall
Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, D.C., United StatesDepartment of Microbiology, Immunology Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C., United States
Sourav Singh
Savitribai Phule Pune University, Pune, Maharashtra, India
W. Augustine Dunn
Boston Children’s Hospital, Boston, United States
Alexandre Drouin
Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
Tomás Di Domenico
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, United Kingdom
Ino de Bruijn
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, United States
David E. Larson
The McDonnell Genome Institute, Washington University, St. Louis, United States
Davide Chicco
Princess Margaret Cancer Centre, Toronto, Canada
Elena Grassi
Transcription and Chromatin Lab, Humanitas University, Rozzano, Italy
Giorgio Gonnella
ZBH-Center for Bioinformatics, MIN-Fakultät, Universität Hamburg, Hamburg, Germany
B. Jaivarsan
Department of Computer Science, Computer science with specialisation in Bioinformatics, VIT University Vellore, India
Liya Wang
Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
Franck Giacomoni
Clermont Auvergne University,INRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont-Ferrand, France
Erik Clarke
Department of Microbiology, University of Pennsylvania, United States
Daniel Blankenberg
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
Camy Tran
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Rob Patro
Department of Computer Science, Stony Brook University, Stony Brook, United States
Sacha Laurent
Institute of Microbiology, Universitary Hospital of Lausanne, Switzerland
Matthew Gopez
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
Bengt Sennblad
Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Jasmijn A. Baaijens
Centrum Wiskunde and Informatica, Amsterdam, Netherlands
Philip Ewels
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
Patrick R. Wright
Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
Oana M. Enache
Broad Institute of MIT and Harvard, Cambridge, United States
Pierrick Roger
CEA, LIST, Laboratory for data analysis and systems’ intelligence, MetaboHUB, France
Will Dampier
Drexel University College of Medicine, Department of Microbiology and Immunology, Philadelphia, United States
David Koppstein
The Kirby Institute of Infection and Immunity, University of New South Wales, Sydney, Australia
Upendra Kumar Devisetty
CyVerse, Bio5 institute, University of Arizona, Tucson, United States
Tobias Rausch
European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany
MacIntosh Cornwell
New York University School of Medicine, New York City, United States
Adrian Emanuel Salatino
Department 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
Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, Illkirch, France
Matthieu Jung
Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, Illkirch, France
Etienne Kornobis
Epigenetic Regulation Unit, Pasteur Institute, Paris, France
Fabio Cumbo
Department of Engineering, Roma Tre University, Rome, ItalyInstitute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council of Italy, Rome, ItalyDepartment of Biochemistry and Molecular Biology, Penn State University, University Park, United States
Bianca Katharina Stöcker
Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Oleksandr Moskalenko
UFIT Research Computing, University of Florida, Gainesville, United States
Daniel R. Bogema
NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
Matthew L. Workentine
Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
Stephen J. Newhouse
Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United KingdomNIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, United KingdomFarr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, United Kingdom
Felipe da Veiga Leprevost
Pathology Department, University of Michigan, Ann Arbor, United States
Kevin Arvai
GeneDx, Gaithersburg, United States
Johannes Köster
Algorithms for reproducible bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-EssenDana 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
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