Bioconda: A sustainable and comprehensive software distribution for the life sciences
Björn Grüning
(1)
,
Ryan Dale
(2)
,
Andreas Sjödin
(3, 4)
,
Brad Chapman
(5)
,
Jillian Rowe
(6)
,
Christopher Tomkins-Tinch
(7)
,
Renan Valieris
(8)
,
Adam Caprez
,
Bérénice Batut
(9)
,
Mathias Haudgaard
,
Thomas Cokelaer
(10)
,
Kyle Beauchamp
,
Brent Pedersen
,
Youri Hoogstrate
(11)
,
Anthony Bretaudeau
(12, 13, 14)
,
Devon Ryan
(15)
,
Gildas Le Corguillé
(16, 17, 18)
,
Dilmurat Yusuf
(19)
,
Sebastian Luna-Valero
,
Rory Kirchner
,
Karel Brinda
(20)
,
Thomas Wollmann
,
Martin Raden
,
Simon 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
,
Joachim Wolff
,
Manuel Holtgrewe
,
Jörg Fallmann
,
Vitor 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 Ruiter
,
Dave Bouvier
,
Simon Gladman
,
Saket Choudhary
,
Nicholas Harding
,
Florian Eggenhofer
,
Arne Kratz
,
Zhuoqing Fang
,
Robert Kleinkauf
,
Henning Timm
,
Peter Cock
,
Enrico Seiler
,
Colin Brislawn
,
Hai Nguyen
,
Endre Bakken Stovner
,
Philip Ewels
,
Matt Chambers
,
James 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 Bogema
,
Fabio Cumbo
,
Liang-Bo Wang
,
David Larson
,
Matthew Workentine
,
Upendra Kumar Devisetty
,
Sacha Laurent
,
Pierrick Roger
,
Xavier Garnier
,
Rasmus Agren
,
Aziz Khan
,
John Eppley
,
Wei Li
,
Bianca Katharina Stöcker
,
Tobias Rausch
,
James Taylor
,
Patrick Wright
,
Adam Taranto
,
Davide Chicco
,
Bengt Sennblad
,
Jasmijn Baaijens
,
Matthew Gopez
,
Nezar Abdennur
,
Iain Milne
,
Jens Preussner
,
Luca Pinello
,
Avi Srivastava
,
Aroon Chande
,
Philip Reiner Kensche
,
Yuri Pirola
,
Michael Knudsen
,
Ino De Bruijn
,
Kai Blin
,
Giorgio Gonnella
,
Oana Enache
,
Vivek Rai
,
Nicholas Waters
,
Saskia Hiltemann
,
Matthew Bendall
,
Christoph Stahl
,
Alistair Miles
,
Yannick Boursin
,
Yasset Perez-Riverol
,
Sebastian Schmeier
,
Erik Clarke
,
Kevin Arvai
,
Matthieu Jung
,
Julien Seiler
,
Eric Rasche
,
Etienne Kornobis
(21)
,
Daniela Beisser
,
Sven Rahmann
,
Alexander Mikheyev
,
Camy Tran
,
Jordi Capellades
,
Christopher Schröder
,
Adrian Emanuel Salatino
,
Simon Dirmeier
,
Timothy Webster
,
Oleksandr Moskalenko
,
Gordon Stephen
,
Johannes Köster
1
University of Freiburg
2 NIH - National Institutes of Health [Bethesda, MD, USA]
3 FOI - Swedish Defence Research Agency [Stockholm]
4 Umeå University = Umeå Universitet
5 Harvard T.H. Chan School of Public Health
6 New York University [Abu Dhabi]
7 Harvard University
8 Hospital Camargo Sao Paulo
9 Department of Computer Science [Freiburg]
10 C3BI - Centre de Bioinformatique, Biostatistique et Biologie Intégrative
11 Erasmus MC - Erasmus University Medical Center [Rotterdam]
12 IAGC - International Aphid Genomics Consortium
13 IGEPP - Institut de Génétique, Environnement et Protection des Plantes
14 Plateforme bioinformatique GenOuest [Rennes]
15 MPI-IE - Max Planck Institute of Immunobiology and Epigenetics
16 ABIMS - ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science
17 SBR - Station biologique de Roscoff = Roscoff Marine Station
18 FR2424 - Fédération de recherche de Roscoff
19 Bioinformatics Group [Freiburg]
20 LIGM - Laboratoire d'Informatique Gaspard-Monge
21 Régulation épigénétique - Epigenetic regulation
2 NIH - National Institutes of Health [Bethesda, MD, USA]
3 FOI - Swedish Defence Research Agency [Stockholm]
4 Umeå University = Umeå Universitet
5 Harvard T.H. Chan School of Public Health
6 New York University [Abu Dhabi]
7 Harvard University
8 Hospital Camargo Sao Paulo
9 Department of Computer Science [Freiburg]
10 C3BI - Centre de Bioinformatique, Biostatistique et Biologie Intégrative
11 Erasmus MC - Erasmus University Medical Center [Rotterdam]
12 IAGC - International Aphid Genomics Consortium
13 IGEPP - Institut de Génétique, Environnement et Protection des Plantes
14 Plateforme bioinformatique GenOuest [Rennes]
15 MPI-IE - Max Planck Institute of Immunobiology and Epigenetics
16 ABIMS - ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science
17 SBR - Station biologique de Roscoff = Roscoff Marine Station
18 FR2424 - Fédération de recherche de Roscoff
19 Bioinformatics Group [Freiburg]
20 LIGM - Laboratoire d'Informatique Gaspard-Monge
21 Régulation épigénétique - Epigenetic regulation
Adam Caprez
- Function : Author
Bérénice Batut
- Function : Author
- PersonId : 1602
- IdHAL : berenice-batut
- ORCID : 0000-0001-9852-1987
- IdRef : 184297370
Mathias Haudgaard
- Function : Author
Kyle Beauchamp
- Function : Author
Brent Pedersen
- Function : Author
Anthony Bretaudeau
- Function : Author
- PersonId : 1688
- IdHAL : anthony-bretaudeau
- ORCID : 0000-0003-0914-2470
- IdRef : 253128358
Sebastian Luna-Valero
- Function : Author
Rory Kirchner
- Function : Author
Thomas Wollmann
- Function : Author
Martin Raden
- Function : Author
Simon Heeringen
- Function : Author
Nicola Soranzo
- Function : Author
Lorena Pantano
- Function : Author
Zachary Charlop-Powers
- Function : Author
Per Unneberg
- Function : Author
Matthias De Smet
- Function : Author
Marcel Martin
- Function : Author
Greg Von Kuster
- Function : Author
Tiago Antao
- Function : Author
Milad Miladi
- Function : Author
Kevin Thornton
- Function : Author
Christian Brueffer
- Function : Author
Marius van Den Beek
- Function : Author
Daniel Maticzka
- Function : Author
Clemens Blank
- Function : Author
Sebastian Will
- Function : Author
Joachim Wolff
- Function : Author
Manuel Holtgrewe
- Function : Author
Jörg Fallmann
- Function : Author
Vitor Piro
- Function : Author
Ilya Shlyakhter
- Function : Author
Ayman Yousif
- Function : Author
Philip Mabon
- Function : Author
Xiao-Ou Zhang
- Function : Author
Wei Shen
- Function : Author
Jennifer Cabral
- Function : Author
Cristel Thomas
- Function : Author
Eric Enns
- Function : Author
Joseph Brown
- Function : Author
Jorrit Boekel
- Function : Author
Mattias De Hollander
- Function : Author
Jerome Kelleher
- Function : Author
Nitesh Turaga
- Function : Author
Julian Ruiter
- Function : Author
Dave Bouvier
- Function : Author
Simon Gladman
- Function : Author
Saket Choudhary
- Function : Author
Nicholas Harding
- Function : Author
Florian Eggenhofer
- Function : Author
Arne Kratz
- Function : Author
Zhuoqing Fang
- Function : Author
Robert Kleinkauf
- Function : Author
Henning Timm
- Function : Author
Peter Cock
- Function : Author
Enrico Seiler
- Function : Author
Colin Brislawn
- Function : Author
Hai Nguyen
- Function : Author
Endre Bakken Stovner
- Function : Author
Philip Ewels
- Function : Author
Matt Chambers
- Function : Author
James Johnson
- Function : Author
Emil Hägglund
- Function : Author
Simon Ye
- Function : Author
Roman Valls Guimera
- Function : Author
Elmar Pruesse
- Function : Author
W. Augustine Dunn
- Function : Author
Lance Parsons
- Function : Author
Rob Patro
- Function : Author
David Koppstein
- Function : Author
Elena Grassi
- Function : Author
Inken Wohlers
- Function : Author
Alex Reynolds
- Function : Author
Macintosh Cornwell
- Function : Author
Nicholas Stoler
- Function : Author
Daniel Blankenberg
- Function : Author
Guowei He
- Function : Author
Marcel Bargull
- Function : Author
Alexander Junge
- Function : Author
Rick Farouni
- Function : Author
Mallory Freeberg
- Function : Author
Sourav Singh
- Function : Author
Daniel Bogema
- Function : Author
Fabio Cumbo
- Function : Author
Liang-Bo Wang
- Function : Author
David Larson
- Function : Author
Matthew Workentine
- Function : Author
Upendra Kumar Devisetty
- Function : Author
Sacha Laurent
- Function : Author
Pierrick Roger
- Function : Author
Xavier Garnier
- Function : Author
Rasmus Agren
- Function : Author
Aziz Khan
- Function : Author
John Eppley
- Function : Author
Wei Li
- Function : Author
Bianca Katharina Stöcker
- Function : Author
Tobias Rausch
- Function : Author
James Taylor
- Function : Author
Patrick Wright
- Function : Author
Adam Taranto
- Function : Author
Davide Chicco
- Function : Author
Bengt Sennblad
- Function : Author
Jasmijn Baaijens
- Function : Author
Matthew Gopez
- Function : Author
Nezar Abdennur
- Function : Author
Iain Milne
- Function : Author
Jens Preussner
- Function : Author
Luca Pinello
- Function : Author
Avi Srivastava
- Function : Author
Aroon Chande
- Function : Author
Philip Reiner Kensche
- Function : Author
Yuri Pirola
- Function : Author
Michael Knudsen
- Function : Author
Ino De Bruijn
- Function : Author
Kai Blin
- Function : Author
Giorgio Gonnella
- Function : Author
Oana Enache
- Function : Author
Vivek Rai
- Function : Author
Nicholas Waters
- Function : Author
Saskia Hiltemann
- Function : Author
Matthew Bendall
- Function : Author
Christoph Stahl
- Function : Author
Alistair Miles
- Function : Author
Yannick Boursin
- Function : Author
Yasset Perez-Riverol
- Function : Author
Sebastian Schmeier
- Function : Author
Erik Clarke
- Function : Author
Kevin Arvai
- Function : Author
Matthieu Jung
- Function : Author
Julien Seiler
- Function : Author
Eric Rasche
- Function : Author
Etienne Kornobis
- Function : Author
- PersonId : 735388
- IdHAL : etienne-kornobis
- ORCID : 0000-0001-7712-8270
Daniela Beisser
- Function : Author
Sven Rahmann
- Function : Author
Alexander Mikheyev
- Function : Author
Camy Tran
- Function : Author
Jordi Capellades
- Function : Author
Christopher Schröder
- Function : Author
Adrian Emanuel Salatino
- Function : Author
Simon Dirmeier
- Function : Author
Timothy Webster
- Function : Author
Oleksandr Moskalenko
- Function : Author
Gordon Stephen
- Function : Author
Johannes Köster
- Function : Author
Abstract
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.
Domains
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