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Bioconda: sustainable and comprehensive software distribution for the life sciences

Nature Methodsvolume 15pages475476 (2018) | Download Citation

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Acknowledgements

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).

Author information

Author notes

  1. These authors contributed equally: Björn Grüning and Ryan Dale.

  2. A full list of authors and affiliations is available as Supplementary Table 1.

Affiliations

  1. Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany

    • Björn Grüning
  2. Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA

    • Ryan Dale
  3. Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden

    • Andreas Sjödin
  4. Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden

    • Andreas Sjödin
  5. Harvard T.H. Chan School of Public Health, Boston, MA, USA

    • Brad A. Chapman
  6. Center for Genomics and Systems Biology, Genomics Core,, NYU Abu Dhabi,, Abu Dhabi,, United Arab Emirates

    • Jillian Rowe
  7. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA

    • Christopher H. Tomkins-Tinch
  8. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    • Christopher H. Tomkins-Tinch
  9. Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, São Paulo, Brazil

    • Renan Valieris
  10. Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg–Essen, Essen, Germany

    • Johannes Köster
  11. Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA

    • Johannes Köster

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Consortia

  1. The Bioconda Team

    Contributions

    J.K. and R.D. wrote the manuscript and conducted the data analysis. K. Beauchamp, C. Brueffer, B.A.C., F. Eggenhofer, B.G., E. Pruesse, M. Raden, J.R., D. Ryan, I. Shlyakter, A.S., C.H.T.-T., and R.V. (in alphabetical order) contributed to writing of the manuscript. D.A. Søndergaard supervised student programmers on writing Conda package recipes and maintaining the connection with ELIXIR. All other members of the Bioconda Team contributed or maintained recipes (author order was determined by the number of commits in October 2017).

    Competing interests

    The authors declare no competing interests.

    Corresponding author

    Correspondence to Johannes Köster.

    Supplementary information

    1. Supplementary information

      Supplementary Results

    2. Reporting summary

    3. Supplementary Table 1

      Consortium author list

    About this article

    Publication history

    Published

    DOI

    https://doi.org/10.1038/s41592-018-0046-7

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