Bioconda: 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; Jaivarsan B; 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:10.1038/s41592-018-0046-7

Bioconda: 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, Jaivarsan B, 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

Research output: Contribution to journal › Article › peer-review

1077 Scopus citations

Original language	English (US)
Pages (from-to)	475-476
Number of pages	2
Journal	Nature Methods
Volume	15
Issue number	7
DOIs	https://doi.org/10.1038/s41592-018-0046-7
State	Published - Jul 1 2018

Bibliographical note

Funding Information:
We thank all contributors, the conda-forge team, and Anaconda Inc. for excellent cooperation. Further, we thank Travis CI (https://travis-ci.com) and Circle CI (https://circleci.com) for providing free Linux and macOS computing capacity. Finally, we thank ELIXIR (https://www.elixir-europe.org) for constant support and donation of staff. This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health (R.D.), the Netherlands Organisation for Scientific Research (NWO) (VENI grant 016. Veni.173.076 to J.K.), the German Research Foundation (SFB 876 to J.K.), and the NYU Abu Dhabi Research Institute for the NYU Abu Dhabi Center for Genomics and Systems Biology, program number CGSB1 (grant to J.R. and A. Yousif).

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10.1038/s41592-018-0046-7

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Dale, R., Grüning, B., Sjödin, A., Rowe, J., Chapman, B. A., Tomkins-Tinch, C. H., Valieris, R., Batut, B., Caprez, A., Cokelaer, T., Yusuf, D., Beauchamp, K. A., Brinda, K., Wollmann, T., Corguillé, G. L., Ryan, D., Bretaudeau, A., Hoogstrate, Y., Pedersen, B. S., ... Köster, J. (2018). Bioconda: Sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475-476. https://doi.org/10.1038/s41592-018-0046-7

Dale, R, Grüning, B, Sjödin, A, Rowe, J, Chapman, BA, Tomkins-Tinch, CH, Valieris, R, Batut, B, Caprez, A, Cokelaer, T, Yusuf, D, Beauchamp, KA, Brinda, K, Wollmann, T, Corguillé, GL, Ryan, D, Bretaudeau, A, Hoogstrate, Y, Pedersen, BS, Heeringen, SV, Raden, M, Luna-Valero, S, Soranzo, N, Smet, MD, Kuster, GV, Kirchner, R, Pantano, L, Charlop-Powers, Z, Thornton, K, Martin, M, Beek, MVD, Maticzka, D, Miladi, M, Will, S, Gravouil, K, Unneberg, P, Brueffer, C, Blank, C, Piro, VC, Wolff, J, Antao, T, Gladman, S, Shlyakhter, I, Hollander, MD, Mabon, P, Shen, W, Boekel, J, Holtgrewe, M, Bouvier, D, de Ruiter, JR, Cabral, J, Choudhary, S, Harding, N, Kleinkauf, R, Enns, E, Eggenhofer, F, Brown, J, Cock, PJA, Timm, H, Thomas, C, Zhang, XO, Chambers, M, Turaga, N, Seiler, E, Brislawn, C, Pruesse, E, Fallmann, J, Kelleher, J, Nguyen, H, Parsons, L, Fang, Z, Stovner, EB, Stoler, N, Ye, S, Wohlers, I, Farouni, R, Freeberg, M, Johnson, JE, Bargull, M, Kensche, PR, Webster, TH, Eppley, JM, Stahl, C, Rose, AS, Reynolds, A, Wang, LB, Garnier, X, Dirmeier, S, Knudsen, M, Taylor, J, Srivastava, A, Rai, V, Agren, R, Junge, A, Guimera, RV, Khan, A, Schmeier, S, He, G, Pinello, L, Hägglund, E, Mikheyev, AS, Preussner, J, Waters, NR, Li, W, Capellades, J, Chande, AT, Pirola, Y, Hiltemann, S, Bendall, ML, Singh, S, Dunn, WA, Drouin, A, Domenico, TD, Bruijn, ID, Larson, DE, Chicco, D, Grassi, E, Gonnella, G, B, J, Wang, L, Giacomoni, F, Clarke, E, Blankenberg, D, Tran, C, Patro, R, Laurent, S, Gopez, M, Sennblad, B, Baaijens, JA, Ewels, P, Wright, PR, Enache, OM, Roger, P, Dampier, W, Koppstein, D, Devisetty, UK, Rausch, T, Cornwell, M, Salatino, AE, Seiler, J, Jung, M, Kornobis, E, Cumbo, F, Stöcker, BK, Moskalenko, O, Bogema, DR, Workentine, ML, Newhouse, SJ, Leprevost, FDV, Arvai, K & Köster, J 2018, 'Bioconda: Sustainable and comprehensive software distribution for the life sciences', Nature Methods, vol. 15, no. 7, pp. 475-476. https://doi.org/10.1038/s41592-018-0046-7

@article{1184a238fa2b4290979bb302fe256e45,

title = "Bioconda: Sustainable and comprehensive software distribution for the life sciences",

author = "Ryan Dale and Bj{\"o}rn Gr{\"u}ning and Andreas Sj{\"o}din and Jillian Rowe and Chapman, \{Brad A.\} and Tomkins-Tinch, \{Christopher H.\} and Renan Valieris and B{\'e}r{\'e}nice Batut and Adam Caprez and Thomas Cokelaer and Dilmurat Yusuf and Beauchamp, \{Kyle A.\} and Karel Brinda and Thomas Wollmann and Corguill{\'e}, \{Gildas Le\} and Devon Ryan and Anthony Bretaudeau and Youri Hoogstrate and Pedersen, \{Brent S.\} and Heeringen, \{Simon van\} and Martin Raden and Sebastian Luna-Valero and Nicola Soranzo and Smet, \{Matthias De\} and Kuster, \{Greg Von\} and Rory Kirchner and Lorena Pantano and Zachary Charlop-Powers and Kevin Thornton and Marcel Martin and Beek, \{Marius van den\} and Daniel Maticzka and Milad Miladi and Sebastian Will and K{\'e}vin Gravouil and Per Unneberg and Christian Brueffer and Clemens Blank and Piro, \{Vitor C.\} and Joachim Wolff and Tiago Antao and Simon Gladman and Ilya Shlyakhter and Hollander, \{Mattias de\} and Philip Mabon and Wei Shen and Jorrit Boekel and Manuel Holtgrewe and Dave Bouvier and \{de Ruiter\}, \{Julian R.\} and Jennifer Cabral and Saket Choudhary and Nicholas Harding and Robert Kleinkauf and Eric Enns and Florian Eggenhofer and Joseph Brown and Cock, \{Peter J.A.\} and Henning Timm and Cristel Thomas and Zhang, \{Xiao Ou\} and Matt Chambers and Nitesh Turaga and Enrico Seiler and Colin Brislawn and Elmar Pruesse and J{\"o}rg Fallmann and Jerome Kelleher and Hai Nguyen and Lance Parsons and Zhuoqing Fang and Stovner, \{Endre Bakken\} and Nicholas Stoler and Simon Ye and Inken Wohlers and Rick Farouni and Mallory Freeberg and Johnson, \{James E\} and Marcel Bargull and Kensche, \{Philip Reiner\} and Webster, \{Timothy H.\} and Eppley, \{John M.\} and Christoph Stahl and Rose, \{Alexander S.\} and Alex Reynolds and Wang, \{Liang Bo\} and Xavier Garnier and Simon Dirmeier and Michael Knudsen and James Taylor and Avi Srivastava and Vivek Rai and Rasmus Agren and Alexander Junge and Guimera, \{Roman Valls\} and Aziz Khan and Sebastian Schmeier and Guowei He and Luca Pinello and Emil H{\"a}gglund and Mikheyev, \{Alexander S.\} and Jens Preussner and Waters, \{Nicholas R.\} and Wei Li and Jordi Capellades and Chande, \{Aroon T.\} and Yuri Pirola and Saskia Hiltemann and Bendall, \{Matthew L.\} and Sourav Singh and Dunn, \{W. Augustine\} and Alexandre Drouin and Domenico, \{Tom{\'a}s Di\} and Bruijn, \{Ino de\} and Larson, \{David E.\} and Davide Chicco and Elena Grassi and Giorgio Gonnella and Jaivarsan B and Liya Wang and Franck Giacomoni and Erik Clarke and Daniel Blankenberg and Camy Tran and Rob Patro and Sacha Laurent and Matthew Gopez and Bengt Sennblad and Baaijens, \{Jasmijn A.\} and Philip Ewels and Wright, \{Patrick R.\} and Enache, \{Oana M.\} and Pierrick Roger and Will Dampier and David Koppstein and Devisetty, \{Upendra Kumar\} and Tobias Rausch and Macintosh Cornwell and Salatino, \{Adrian Emanuel\} and Julien Seiler and Matthieu Jung and Etienne Kornobis and Fabio Cumbo and St{\"o}cker, \{Bianca Katharina\} and Oleksandr Moskalenko and Bogema, \{Daniel R.\} and Workentine, \{Matthew L.\} and Newhouse, \{Stephen J.\} and Leprevost, \{Felipe da Veiga\} and Kevin Arvai and Johannes K{\"o}ster",

note = "Funding Information: We thank all contributors, the conda-forge team, and Anaconda Inc. for excellent cooperation. Further, we thank Travis CI (https://travis-ci.com) and Circle CI (https://circleci.com) for providing free Linux and macOS computing capacity. Finally, we thank ELIXIR (https://www.elixir-europe.org) for constant support and donation of staff. This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health (R.D.), the Netherlands Organisation for Scientific Research (NWO) (VENI grant 016. Veni.173.076 to J.K.), the German Research Foundation (SFB 876 to J.K.), and the NYU Abu Dhabi Research Institute for the NYU Abu Dhabi Center for Genomics and Systems Biology, program number CGSB1 (grant to J.R. and A. Yousif).",

year = "2018",

month = jul,

day = "1",

doi = "10.1038/s41592-018-0046-7",

language = "English (US)",

volume = "15",

pages = "475--476",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "7",

}

TY - JOUR

T1 - Bioconda

T2 - Sustainable and comprehensive software distribution for the life sciences

AU - Dale, Ryan

AU - Grüning, Björn

AU - Sjödin, Andreas

AU - Rowe, Jillian

AU - Chapman, Brad A.

AU - Tomkins-Tinch, Christopher H.

AU - Valieris, Renan

AU - Batut, Bérénice

AU - Caprez, Adam

AU - Cokelaer, Thomas

AU - Yusuf, Dilmurat

AU - Beauchamp, Kyle A.

AU - Brinda, Karel

AU - Wollmann, Thomas

AU - Corguillé, Gildas Le

AU - Ryan, Devon

AU - Bretaudeau, Anthony

AU - Hoogstrate, Youri

AU - Pedersen, Brent S.

AU - Heeringen, Simon van

AU - Raden, Martin

AU - Luna-Valero, Sebastian

AU - Soranzo, Nicola

AU - Smet, Matthias De

AU - Kuster, Greg Von

AU - Kirchner, Rory

AU - Pantano, Lorena

AU - Charlop-Powers, Zachary

AU - Thornton, Kevin

AU - Martin, Marcel

AU - Beek, Marius van den

AU - Maticzka, Daniel

AU - Miladi, Milad

AU - Will, Sebastian

AU - Gravouil, Kévin

AU - Unneberg, Per

AU - Brueffer, Christian

AU - Blank, Clemens

AU - Piro, Vitor C.

AU - Wolff, Joachim

AU - Antao, Tiago

AU - Gladman, Simon

AU - Shlyakhter, Ilya

AU - Hollander, Mattias de

AU - Mabon, Philip

AU - Shen, Wei

AU - Boekel, Jorrit

AU - Holtgrewe, Manuel

AU - Bouvier, Dave

AU - de Ruiter, Julian R.

AU - Cabral, Jennifer

AU - Choudhary, Saket

AU - Harding, Nicholas

AU - Kleinkauf, Robert

AU - Enns, Eric

AU - Eggenhofer, Florian

AU - Brown, Joseph

AU - Cock, Peter J.A.

AU - Timm, Henning

AU - Thomas, Cristel

AU - Zhang, Xiao Ou

AU - Chambers, Matt

AU - Turaga, Nitesh

AU - Seiler, Enrico

AU - Brislawn, Colin

AU - Pruesse, Elmar

AU - Fallmann, Jörg

AU - Kelleher, Jerome

AU - Nguyen, Hai

AU - Parsons, Lance

AU - Fang, Zhuoqing

AU - Stovner, Endre Bakken

AU - Stoler, Nicholas

AU - Ye, Simon

AU - Wohlers, Inken

AU - Farouni, Rick

AU - Freeberg, Mallory

AU - Johnson, James E

AU - Bargull, Marcel

AU - Kensche, Philip Reiner

AU - Webster, Timothy H.

AU - Eppley, John M.

AU - Stahl, Christoph

AU - Rose, Alexander S.

AU - Reynolds, Alex

AU - Wang, Liang Bo

AU - Garnier, Xavier

AU - Dirmeier, Simon

AU - Knudsen, Michael

AU - Taylor, James

AU - Srivastava, Avi

AU - Rai, Vivek

AU - Agren, Rasmus

AU - Junge, Alexander

AU - Guimera, Roman Valls

AU - Khan, Aziz

AU - Schmeier, Sebastian

AU - He, Guowei

AU - Pinello, Luca

AU - Hägglund, Emil

AU - Mikheyev, Alexander S.

AU - Preussner, Jens

AU - Waters, Nicholas R.

AU - Li, Wei

AU - Capellades, Jordi

AU - Chande, Aroon T.

AU - Pirola, Yuri

AU - Hiltemann, Saskia

AU - Bendall, Matthew L.

AU - Singh, Sourav

AU - Dunn, W. Augustine

AU - Drouin, Alexandre

AU - Domenico, Tomás Di

AU - Bruijn, Ino de

AU - Larson, David E.

AU - Chicco, Davide

AU - Grassi, Elena

AU - Gonnella, Giorgio

AU - B, Jaivarsan

AU - Wang, Liya

AU - Giacomoni, Franck

AU - Clarke, Erik

AU - Blankenberg, Daniel

AU - Tran, Camy

AU - Patro, Rob

AU - Laurent, Sacha

AU - Gopez, Matthew

AU - Sennblad, Bengt

AU - Baaijens, Jasmijn A.

AU - Ewels, Philip

AU - Wright, Patrick R.

AU - Enache, Oana M.

AU - Roger, Pierrick

AU - Dampier, Will

AU - Koppstein, David

AU - Devisetty, Upendra Kumar

AU - Rausch, Tobias

AU - Cornwell, Macintosh

AU - Salatino, Adrian Emanuel

AU - Seiler, Julien

AU - Jung, Matthieu

AU - Kornobis, Etienne

AU - Cumbo, Fabio

AU - Stöcker, Bianca Katharina

AU - Moskalenko, Oleksandr

AU - Bogema, Daniel R.

AU - Workentine, Matthew L.

AU - Newhouse, Stephen J.

AU - Leprevost, Felipe da Veiga

AU - Arvai, Kevin

AU - Köster, Johannes

N1 - Funding Information: We thank all contributors, the conda-forge team, and Anaconda Inc. for excellent cooperation. Further, we thank Travis CI (https://travis-ci.com) and Circle CI (https://circleci.com) for providing free Linux and macOS computing capacity. Finally, we thank ELIXIR (https://www.elixir-europe.org) for constant support and donation of staff. This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health (R.D.), the Netherlands Organisation for Scientific Research (NWO) (VENI grant 016. Veni.173.076 to J.K.), the German Research Foundation (SFB 876 to J.K.), and the NYU Abu Dhabi Research Institute for the NYU Abu Dhabi Center for Genomics and Systems Biology, program number CGSB1 (grant to J.R. and A. Yousif).

PY - 2018/7/1

Y1 - 2018/7/1

UR - https://www.scopus.com/pages/publications/85049501214

UR - https://www.scopus.com/pages/publications/85049501214#tab=citedBy

U2 - 10.1038/s41592-018-0046-7

DO - 10.1038/s41592-018-0046-7

M3 - Article

C2 - 29967506

AN - SCOPUS:85049501214

SN - 1548-7091

VL - 15

SP - 475

EP - 476

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -

Bioconda: Sustainable and comprehensive software distribution for the life sciences

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