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QurvE: user-friendly software for the analysis of biological growth and fluorescence data

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Fig. 1: QurvE enables robust, high-throughput analysis of growth and fluorescence data.

Data availability

Input data used as examples in this article are embedded in the R package as part of the function help documentation and the accompanying manuals. Further example files and data therein can be found at https://github.com/NicWir/QurvE/tree/master/examples.

Code availability

QurvE is published under the GNU General Public License version 3 and is available as an R package on the Comprehensive R Archive Network (CRAN). The source code, along with the most recent development version, can be found at https://github.com/NicWir/QurvE. Documentation, tutorials, troubleshooting guidelines, and the Shiny app, which can be installed as standalone software, can be accessed and downloaded from https://nicwir.github.io/QurvE. Additionally, the Shiny app is available as a web-based application accessible through any browser at https://www.qurveanalysis.com/.

References

  1. Neidhardt, F. C., Ingraham, J. L. & Schaechter, M. Physiology of the Bacterial Cell: A Molecular Approach (Sinauer Associates, 1990).

  2. Hall, B. G., Acar, H., Nandipati, A. & Barlow, M. Mol. Biol. Evol. 31, 232–238 (2014).

  3. Wirth, N. T. et al. Metab. Eng. 74, 83–97 (2022).

  4. Neidhardt, F. C. J. Bacteriol. 181, 7405–7408 (1999).

  5. Gurdo, N., Volke, D. C. & Nikel, P. I. Trends Biotechnol. 40, 1148–1159 (2022).

  6. Swain, P. S. et al. Nat. Commun. 7, 13766 (2016).

  7. Kahm, M., Hasenbrink, G., Lichtenberg-Fraté, H., Ludwig, J. & Kschischo, M. J. Stat. Software 33, 1–21 (2010).

  8. Huang, L. Food Microbiol. 28, 770–776 (2011).

  9. Baranyi, J. & Roberts, T. A. Int. J. Food Microbiol. 26, 199–218 (1995).

  10. Theil, H. in Henri Theil’s Contributions to Economics and Econometrics: Econometric Theory and Methodology (eds Raj, B. & Koerts, J.) 345–381 (Springer, 1992).

  11. Ritz, C., Baty, F., Streibig, J. C. & Gerhard, D. PLoS ONE 10, e0146021 (2015).

  12. Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J. & Voigt, C. A. Nat. Chem. Biol. 15, 196–204 (2019).

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Acknowledgements

We are indebted to the growing community of QurvE users for their feedback and suggestions. This study was supported by grants from the Novo Nordisk Foundation (NNF20CC0035580, LiFe (NNF18OC0034818) and TARGET (NNF21OC0067996)), the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 814418 (SinFonia) and the Cystic Fibrosis Trust, Strategic Research Centre Award–2019–SRC017 to P.I.N.

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Authors and Affiliations

  1. The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark

    Nicolas T. Wirth, Jonathan Funk, Stefano Donati & Pablo I. Nikel

Authors
  1. Nicolas T. Wirth
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  2. Jonathan Funk
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  3. Stefano Donati
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  4. Pablo I. Nikel
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Contributions

N.T.W. conceptualized and designed the project and is the main developer and maintainer of the QurvE package; J.F. contributed to writing the code for the Shiny app; S.D. contributed to the design, testing and documentation; N.T.W. and P.I.N wrote the paper; P.I.N. supervised the whole project and secured funding.

Corresponding author

Correspondence to Pablo I. Nikel.

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The authors declare no competing interests.

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Nature Protocols thanks Michael Kuhn and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Wirth, N.T., Funk, J., Donati, S. et al. QurvE: user-friendly software for the analysis of biological growth and fluorescence data. Nat Protoc 18, 2401–2403 (2023). https://doi.org/10.1038/s41596-023-00850-7

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