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Bioconda: sustainable and comprehensive software distribution for the life sciences

Authors :
Dale R.
Gruning B.
Sjodin 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.
Corguille G. L.
Ryan D.
Bretaudeau A.
Hoogstrate Y.
Pedersen B. S.
Heeringen S.
Raden M.
Luna-Valero S.
Soranzo N.
Smet M. D.
Kuster G. V.
Kirchner R.
Pantano L.
Charlop-Powers Z.
Thornton K.
Martin M.
Beek M. D.
Maticzka D.
Miladi M.
Will S.
Gravouil K.
Unneberg P.
Brueffer C.
Blank C.
Piro V. C.
Wolff J.
Antao T.
Gladman S.
Shlyakhter I.
Hollander M.
Mabon P.
Shen W.
Boekel J.
Holtgrewe M.
Bouvier D.
de Ruiter J. R.
Cabral J.
Choudhary S.
Harding N.
Kleinkauf R.
Enns E.
Eggenhofer F.
Brown J.
Cock P. J. A.
Timm H.
Thomas C.
Zhang X. -O.
Chambers M.
Turaga N.
Seiler E.
Brislawn C.
Pruesse E.
Fallmann J.
Kelleher J.
Nguyen H.
Parsons L.
Fang Z.
Stovner E. B.
Stoler N.
Ye S.
Wohlers I.
Farouni R.
Freeberg M.
Johnson J. E.
Bargull M.
Kensche P. R.
Webster T. H.
Eppley J. M.
Stahl C.
Rose A. S.
Reynolds A.
Wang L. -B.
Garnier X.
Dirmeier S.
Knudsen M.
Taylor J.
Srivastava A.
Rai V.
Agren R.
Junge A.
Guimera R. V.
Khan A.
Schmeier S.
He G.
Pinello L.
Hagglund E.
Mikheyev A. S.
Preussner J.
Waters N. R.
Li W.
Capellades J.
Chande A. T.
Pirola Y.
Hiltemann S.
Bendall M. L.
Singh S.
Dunn W. A.
Drouin A.
Domenico T. D.
Bruijn I.
Larson D. E.
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 J. A.
Ewels P.
Wright P. R.
Enache O. M.
Roger P.
Dampier W.
Koppstein D.
Devisetty U. K.
Rausch T.
Cornwell M.
Salatino A. E.
Seiler J.
Jung M.
Kornobis E.
Cumbo F.
Stocker B. K.
Moskalenko O.
Bogema D. R.
Workentine M. L.
Newhouse S. J.
Leprevost F. D. V.
Arvai K.
Koster J.
Albert-Ludwigs-Universität Freiburg
National Institutes of Health [Bethesda] (NIH)
Swedish Defence Research Agency [Stockholm] (FOI)
Umeå University
Harvard T.H. Chan School of Public Health
New York University [Abu Dhabi]
NYU System (NYU)
Harvard University [Cambridge]
Hospital Camargo Sao Paulo
Partenaires INRAE
University of Duisburg-Essen
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).
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.
Etienne Kornobis (Epigenetic Regulation Unit, Institut Pasteur, Paris, France) fait partie de Bioconda Team
Bioinformatics Group, Department ​ ​ of ​ ​ Computer ​ ​ Science
University of Freiburg [Freiburg]
Laboratory of Cellular and Developmental Biology (LCDB)
NIDDK, NIH
Department of Organismic and Evolutionary Biology
Broad Institute of MIT and Harvard (BROAD INSTITUTE)
Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston]
Microbiologie Environnement Digestif Santé (MEDIS)
INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Umea Plant Science Center (UPSC)
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU)
Laboratoire Microorganismes : Génome et Environnement (LMGE)
Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)
Harvard University
Universität Duisburg-Essen = University of Duisburg-Essen [Essen]
Dale, R
Gruning, B
Sjodin, A
Rowe, J
Chapman, B
Tomkins-Tinch, C
Valieris, R
Batut, B
Caprez, A
Cokelaer, T
Yusuf, D
Beauchamp, K
Brinda, K
Wollmann, T
Corguille, G
Ryan, D
Bretaudeau, A
Hoogstrate, Y
Pedersen, B
Heeringen, S
Raden, M
Luna-Valero, S
Soranzo, N
Smet, M
Kuster, G
Kirchner, R
Pantano, L
Charlop-Powers, Z
Thornton, K
Martin, M
Beek, M
Maticzka, D
Miladi, M
Will, S
Gravouil, K
Unneberg, P
Brueffer, C
Blank, C
Piro, V
Wolff, J
Antao, T
Gladman, S
Shlyakhter, I
Hollander, M
Mabon, P
Shen, W
Boekel, J
Holtgrewe, M
Bouvier, D
de Ruiter, J
Cabral, J
Choudhary, S
Harding, N
Kleinkauf, R
Enns, E
Eggenhofer, F
Brown, J
Cock, P
Timm, H
Thomas, C
Zhang, X
Chambers, M
Turaga, N
Seiler, E
Brislawn, C
Pruesse, E
Fallmann, J
Kelleher, J
Nguyen, H
Parsons, L
Fang, Z
Stovner, E
Stoler, N
Ye, S
Wohlers, I
Farouni, R
Freeberg, M
Johnson, J
Bargull, M
Kensche, P
Webster, T
Eppley, J
Stahl, C
Rose, A
Reynolds, A
Wang, L
Garnier, X
Dirmeier, S
Knudsen, M
Taylor, J
Srivastava, A
Rai, V
Agren, R
Junge, A
Guimera, R
Khan, A
Schmeier, S
He, G
Pinello, L
Hagglund, E
Mikheyev, A
Preussner, J
Waters, N
Li, W
Capellades, J
Chande, A
Pirola, Y
Hiltemann, S
Bendall, M
Singh, S
Dunn, W
Drouin, A
Domenico, T
Bruijn, I
Larson, D
Chicco, D
Grassi, E
Gonnella, G
B, J
Giacomoni, F
Clarke, E
Blankenberg, D
Tran, C
Patro, R
Laurent, S
Gopez, M
Sennblad, B
Baaijens, J
Ewels, P
Wright, P
Enache, O
Roger, P
Dampier, W
Koppstein, D
Devisetty, U
Rausch, T
Cornwell, M
Salatino, A
Seiler, J
Jung, M
Kornobis, E
Cumbo, F
Stocker, B
Moskalenko, O
Bogema, D
Workentine, M
Newhouse, S
Leprevost, F
Arvai, K
Koster, J
Urology
Pathology
Source :
Nature Methods, Nature Methods, Nature Publishing Group, 2018, 15 (7), pp.475-476. ⟨10.1038/s41592-018-0046-7⟩, Nature Methods, Nature Publishing Group, 2018, 15 (7), pp.475-476, Nature Methods, 2018, 15 (7), pp.475-476. ⟨10.1038/s41592-018-0046-7⟩, Nature Methods, 15(7), 475-476. Nature Publishing Group
Publication Year :
2018
Publisher :
HAL CCSD, 2018.

Abstract

International audience; 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 o ers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bio- conda improves analysis reproducibility by allowing users to de ne isolated environments with de ned software versions, all of which are easily installed and managed without administrative privileges.

Subjects

Subjects :
0301 basic medicine
Computer science
[SDV]Life Sciences [q-bio]
Medizin
computer.software_genre
Biochemistry
User-Computer Interface
03 medical and health sciences
0302 clinical medicine
Software system
Molecular Biology
ComputingMilieux_MISCELLANEOUS
Social software engineering
Database
business.industry
Software development
INF/01 - INFORMATICA
Computational Biology
Cell Biology
Software distribution
030104 developmental biology
Software construction
[SDE]Environmental Sciences
Package development process
Backporting
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
business
computer
Software
030217 neurology & neurosurgery
Biotechnology

Details

Language :
English
ISSN :
15487091 and 15487105
Database :
OpenAIRE
Journal :
Nature Methods, Nature Methods, Nature Publishing Group, 2018, 15 (7), pp.475-476. ⟨10.1038/s41592-018-0046-7⟩, Nature Methods, Nature Publishing Group, 2018, 15 (7), pp.475-476, Nature Methods, 2018, 15 (7), pp.475-476. ⟨10.1038/s41592-018-0046-7⟩, Nature Methods, 15(7), 475-476. Nature Publishing Group
Accession number :
edsair.doi.dedup.....183f2a9d867a8a3bf8cb7ac58bc6740e
Full Text :
https://doi.org/10.1038/s41592-018-0046-7⟩
Full Text Access
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