Bioconda: sustainable and comprehensive software distribution for the life sciences

Björn  Grüning; Ryan Dale; Andreas Sjödin; Brad A. Chapman; Jillian Rowe; Christopher H. Tomkins-Tinch; Renan Valieris; Johannes Köster; Kai Blin; Mathias Haudgaard; Arne Kratz; Alexander Junge; Michael Knudsen

doi:10.1038/s41592-018-0046-7

Bioconda: sustainable and comprehensive software distribution for the life sciences

Björn Grüning , Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster, Kai Blin, Mathias Haudgaard, Arne Kratz, Alexander Junge, Michael Knudsen

Novo Nordisk Foundation Center for Biosustainability

Research output: Contribution to journal › Comment/debate › Research › peer-review

Abstract

To the Editor: Bioinformatics software comes in a variety of programming languages and requires diverse installation methods. This heterogeneity makes management of a software stack complicated, error-prone, and inordinately time-consuming. Whereas software deployment has traditionally been handled by administrators, ensuring the reproducibility of data analyses1,2,3 requires that the researcher be able to maintain full control of the software environment, rapidly modify it without administrative privileges, and reproduce the same software stack on different machines.

Original language	English
Journal	Nature Methods
Volume	15
Pages (from-to)	475-476
ISSN	1548-7091
DOIs	https://doi.org/10.1038/s41592-018-0046-7
Publication status	Published - 2018

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Grüning , Björn ; Dale, Ryan ; Sjödin, Andreas ; Chapman, Brad A. ; Rowe, Jillian ; Tomkins-Tinch, Christopher H. ; Valieris, Renan ; Köster, Johannes ; Blin, Kai ; Haudgaard, Mathias ; Kratz, Arne ; Junge, Alexander ; Knudsen, Michael. / Bioconda: sustainable and comprehensive software distribution for the life sciences. In: Nature Methods. 2018 ; Vol. 15. pp. 475-476.

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abstract = "To the Editor: Bioinformatics software comes in a variety of programming languages and requires diverse installation methods. This heterogeneity makes management of a software stack complicated, error-prone, and inordinately time-consuming. Whereas software deployment has traditionally been handled by administrators, ensuring the reproducibility of data analyses1,2,3 requires that the researcher be able to maintain full control of the software environment, rapidly modify it without administrative privileges, and reproduce the same software stack on different machines.",

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Bioconda: sustainable and comprehensive software distribution for the life sciences. / Grüning , Björn ; Dale, Ryan; Sjödin, Andreas; Chapman, Brad A.; Rowe, Jillian; Tomkins-Tinch, Christopher H.; Valieris, Renan; Köster, Johannes; Blin, Kai; Haudgaard, Mathias; Kratz, Arne; Junge, Alexander; Knudsen, Michael.

In: Nature Methods, Vol. 15, 2018, p. 475-476.

Research output: Contribution to journal › Comment/debate › Research › peer-review

TY - JOUR

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

AU - Grüning , Björn

AU - Dale, Ryan

AU - Sjödin, Andreas

AU - Chapman, Brad A.

AU - Rowe, Jillian

AU - Tomkins-Tinch, Christopher H.

AU - Valieris, Renan

AU - Köster, Johannes

AU - Blin, Kai

AU - Haudgaard, Mathias

AU - Kratz, Arne

AU - Junge, Alexander

AU - Knudsen, Michael

PY - 2018

Y1 - 2018

N2 - To the Editor: Bioinformatics software comes in a variety of programming languages and requires diverse installation methods. This heterogeneity makes management of a software stack complicated, error-prone, and inordinately time-consuming. Whereas software deployment has traditionally been handled by administrators, ensuring the reproducibility of data analyses1,2,3 requires that the researcher be able to maintain full control of the software environment, rapidly modify it without administrative privileges, and reproduce the same software stack on different machines.

AB - To the Editor: Bioinformatics software comes in a variety of programming languages and requires diverse installation methods. This heterogeneity makes management of a software stack complicated, error-prone, and inordinately time-consuming. Whereas software deployment has traditionally been handled by administrators, ensuring the reproducibility of data analyses1,2,3 requires that the researcher be able to maintain full control of the software environment, rapidly modify it without administrative privileges, and reproduce the same software stack on different machines.

U2 - 10.1038/s41592-018-0046-7

DO - 10.1038/s41592-018-0046-7

M3 - Comment/debate

C2 - 29967506

VL - 15

SP - 475

EP - 476

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

ER -

Bioconda: sustainable and comprehensive software distribution for the life sciences

Abstract

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