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

Björn Grüning; Ryan Dale; Andreas Sjödin; Brad Chapman; Jillian Rowe; Christopher Tomkins-Tinch; Renan Valieris; Adam Caprez; Bérénice Batut; Mathias Haudgaard; Thomas Cokelaer; Kyle Beauchamp; Brent Pedersen; Youri Hoogstrate; Anthony Bretaudeau; Devon Ryan; Gildas Le Corguillé; Dilmurat Yusuf; Sebastian Luna-Valero; Rory Kirchner; Karel Brinda; Thomas Wollmann; Martin Raden; Simon 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 der Beek; Daniel Maticzka; Clemens Blank; Sebastian Will; Kévin Gravouil; 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 de 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; 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; Tomás Di Domenico; Julien Seiler; Eric Rasche; Etienne Kornobis; 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

doi:10.1101/207092

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

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad Chapman, Jillian Rowe, Christopher Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle Beauchamp, Brent Pedersen, Youri Hoogstrate, Anthony Bretaudeau, Devon Ryan, Gildas Le Corguillé, Dilmurat Yusuf, Sebastian Luna-Valero, Rory KirchnerKarel Brinda, Thomas Wollmann, Martin Raden, Simon 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 der Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, Kévin Gravouil, 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 de 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, 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, Tomás Di Domenico, Julien Seiler, Eric Rasche, Etienne Kornobis, 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

Breastcancer-genetics

Research output: Working paper/Preprint › Preprint (in preprint archive)

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 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.

Original language	English
Publisher	bioRxiv
Number of pages	13
DOIs	https://doi.org/10.1101/207092
Publication status	Published - 2017 Oct 21

Subject classification (UKÄ)

Bioinformatics (Computational Biology)
Bioinformatics and Systems Biology
Other Medical Sciences not elsewhere specified

Keywords

Bioinformatics
Bioinformatics tools
Computational biology
Software distribution

Access to Document

10.1101/207092Licence: CC BY-NC-ND

1 Letter

Bioconda: sustainable and comprehensive software distribution for the life sciences
Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., Bioconda Team & Brueffer, C., 2018 Jul 2, In: Nature Methods. 15, 7, p. 475-476 2 p.
Research output: Contribution to journal › Letter › peer-review

Cite this

Grüning, B., Dale, R., Sjödin, A., Chapman, B., Rowe, J., Tomkins-Tinch, C., Valieris, R., Caprez, A., Batut, B., Haudgaard, M., Cokelaer, T., Beauchamp, K., Pedersen, B., Hoogstrate, Y., Bretaudeau, A., Ryan, D., Le Corguillé, G., Yusuf, D., Luna-Valero, S., ... Köster, J. (2017). Bioconda: A sustainable and comprehensive software distribution for the life sciences. bioRxiv. https://doi.org/10.1101/207092

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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 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.",

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Grüning, B, Dale, R, Sjödin, A, Chapman, B, Rowe, J, Tomkins-Tinch, C, Valieris, R, Caprez, A, Batut, B, Haudgaard, M, Cokelaer, T, Beauchamp, K, Pedersen, B, Hoogstrate, Y, Bretaudeau, A, Ryan, D, Le Corguillé, G, Yusuf, D, Luna-Valero, S, Kirchner, R, Brinda, K, Wollmann, T, Raden, M, van Heeringen, S, Soranzo, N, Pantano, L, Charlop-Powers, Z, Unneberg, P, De Smet, M, Martin, M, Von Kuster, G, Antao, T, Miladi, M, Thornton, K, Brueffer, C, van der Beek, M, Maticzka, D, Blank, C, Will, S, Gravouil, K, Wolff, J, Holtgrewe, M, Fallmann, J, Piro, V, Shlyakhter, I, Yousif, A, Mabon, P, Zhang, X-O, Shen, W, Cabral, J, Thomas, C, Enns, E, Brown, J, Boekel, J, de Hollander, M, Kelleher, J, Turaga, N, de Ruiter, J, Bouvier, D, Gladman, S, Choudhary, S, Harding, N, Eggenhofer, F, Kratz, A, Fang, Z, Kleinkauf, R, Timm, H, Cock, P, Seiler, E, Brislawn, C, Nguyen, H, Bakken Stovner, E, Ewels, P, Chambers, M, Johnson, J, Hägglund, E, Ye, S, Valls Guimera, R, Pruesse, E, Dunn, A, Parsons, L, Patro, R, Koppstein, D, Grassi, E, Wohlers, I, Reynolds, A, Cornwell, M, Stoler, N, Blankenberg, D, He, G, Bargull, M, Junge, A, Farouni, R, Freeberg, M, Singh, S, Bogema, D, Cumbo, F, Wang, L-B, Larson, D, Workentine, M, Kumar Devisetty, U, Laurent, S, Roger, P, Garnier, X, Agren, R, Khan, A, Eppley, J, Li, W, Stöcker, BK, Rausch, T, Taylor, J, Wright, P, Taranto, A, Chicco, D, Sennblad, B, Baaijens, J, Gopez, M, Abdennur, N, Milne, I, Preussner, J, Pinello, L, Srivastava, A, Chande, A, Kensche, PR, Pirola, Y, Knudsen, M, de Bruijn, I, Blin, K, Gonnella, G, Enache, O, Rai, V, Waters, N, Hiltemann, S, Bendall, M, Stahl, C, Miles, A, Boursin, Y, Perez-Riverol, Y, Schmeier, S, Clarke, E, Arvai, K, Jung, M, Di Domenico, T, Seiler, J, Rasche, E, Kornobis, E, Beisser, D, Rahmann, S, Mikheyev, A, Tran, C, Capellades, J, Schröder, C, Salatino, AE, Dirmeier, S, Webster, T, Moskalenko, O, Stephen, G & Köster, J 2017 'Bioconda: A sustainable and comprehensive software distribution for the life sciences' bioRxiv. https://doi.org/10.1101/207092

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T1 - Bioconda: A sustainable and comprehensive software distribution for the life sciences

AU - Grüning, Björn

AU - Dale, Ryan

AU - Sjödin, Andreas

AU - Chapman, Brad

AU - Rowe, Jillian

AU - Tomkins-Tinch, Christopher

AU - Valieris, Renan

AU - Caprez, Adam

AU - Batut, Bérénice

AU - Haudgaard, Mathias

AU - Cokelaer, Thomas

AU - Beauchamp, Kyle

AU - Pedersen, Brent

AU - Hoogstrate, Youri

AU - Bretaudeau, Anthony

AU - Ryan, Devon

AU - Le Corguillé, Gildas

AU - Yusuf, Dilmurat

AU - Luna-Valero, Sebastian

AU - Kirchner, Rory

AU - Brinda, Karel

AU - Wollmann, Thomas

AU - Raden, Martin

AU - van Heeringen, Simon

AU - Soranzo, Nicola

AU - Pantano, Lorena

AU - Charlop-Powers, Zachary

AU - Unneberg, Per

AU - De Smet, Matthias

AU - Martin, Marcel

AU - Von Kuster, Greg

AU - Antao, Tiago

AU - Miladi, Milad

AU - Thornton, Kevin

AU - Brueffer, Christian

AU - van der Beek, Marius

AU - Maticzka, Daniel

AU - Blank, Clemens

AU - Will, Sebastian

AU - Gravouil, Kévin

AU - Wolff, Joachim

AU - Holtgrewe, Manuel

AU - Fallmann, Jörg

AU - Piro, Vitor

AU - Shlyakhter, Ilya

AU - Yousif, Ayman

AU - Mabon, Philip

AU - Zhang, Xiao-Ou

AU - Shen, Wei

AU - Cabral, Jennifer

AU - Thomas, Cristel

AU - Enns, Eric

AU - Brown, Joseph

AU - Boekel, Jorrit

AU - de Hollander, Mattias

AU - Kelleher, Jerome

AU - Turaga, Nitesh

AU - de Ruiter, Julian

AU - Bouvier, Dave

AU - Gladman, Simon

AU - Choudhary, Saket

AU - Harding, Nicholas

AU - Eggenhofer, Florian

AU - Kratz, Arne

AU - Fang, Zhuoqing

AU - Kleinkauf, Robert

AU - Timm, Henning

AU - Cock, Peter

AU - Seiler, Enrico

AU - Brislawn, Colin

AU - Nguyen, Hai

AU - Bakken Stovner, Endre

AU - Ewels, Philip

AU - Chambers, Matt

AU - Johnson, James

AU - Hägglund, Emil

AU - Ye, Simon

AU - Valls Guimera, Roman

AU - Pruesse, Elmar

AU - Dunn, Augustine

AU - Parsons, Lance

AU - Patro, Rob

AU - Koppstein, David

AU - Grassi, Elena

AU - Wohlers, Inken

AU - Reynolds, Alex

AU - Cornwell, MacIntosh

AU - Stoler, Nicholas

AU - Blankenberg, Daniel

AU - He, Guowei

AU - Bargull, Marcel

AU - Junge, Alexander

AU - Farouni, Rick

AU - Freeberg, Mallory

AU - Singh, Sourav

AU - Bogema, Daniel

AU - Cumbo, Fabio

AU - Wang, Liang-Bo

AU - Larson, David

AU - Workentine, Matthew

AU - Kumar Devisetty, Upendra

AU - Laurent, Sacha

AU - Roger, Pierrick

AU - Garnier, Xavier

AU - Agren, Rasmus

AU - Khan, Aziz

AU - Eppley, John

AU - Li, Wei

AU - Stöcker, Bianca Katharina

AU - Rausch, Tobias

AU - Taylor, James

AU - Wright, Patrick

AU - Taranto, Adam

AU - Chicco, Davide

AU - Sennblad, Bengt

AU - Baaijens, Jasmijn

AU - Gopez, Matthew

AU - Abdennur, Nezar

AU - Milne, Iain

AU - Preussner, Jens

AU - Pinello, Luca

AU - Srivastava, Avi

AU - Chande, Aroon

AU - Kensche, Philip Reiner

AU - Pirola, Yuri

AU - Knudsen, Michael

AU - de Bruijn, Ino

AU - Blin, Kai

AU - Gonnella, Giorgio

AU - Enache, Oana

AU - Rai, Vivek

AU - Waters, Nicholas

AU - Hiltemann, Saskia

AU - Bendall, Matthew

AU - Stahl, Christoph

AU - Miles, Alistair

AU - Boursin, Yannick

AU - Perez-Riverol, Yasset

AU - Schmeier, Sebastian

AU - Clarke, Erik

AU - Arvai, Kevin

AU - Jung, Matthieu

AU - Di Domenico, Tomás

AU - Seiler, Julien

AU - Rasche, Eric

AU - Kornobis, Etienne

AU - Beisser, Daniela

AU - Rahmann, Sven

AU - Mikheyev, Alexander

AU - Tran, Camy

AU - Capellades, Jordi

AU - Schröder, Christopher

AU - Salatino, Adrian Emanuel

AU - Dirmeier, Simon

AU - Webster, Timothy

AU - Moskalenko, Oleksandr

AU - Stephen, Gordon

AU - Köster, Johannes

PY - 2017/10/21

Y1 - 2017/10/21

N2 - 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 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.

AB - 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 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.

KW - Bioinformatics

KW - Bioinformatics tools

KW - Computational biology

KW - Software distribution

U2 - 10.1101/207092

DO - 10.1101/207092

M3 - Preprint (in preprint archive)

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

PB - bioRxiv

ER -

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

Abstract

Subject classification (UKÄ)

Keywords

Access to Document

Fingerprint

Research output

Bioconda: sustainable and comprehensive software distribution for the life sciences

Cite this