diff --git a/paper/paper.md b/paper/paper.md index 1f79ea8..bcabaa9 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -23,15 +23,15 @@ authors: orcid: 0000-0001-5585-6277 affiliation: "2, 3, 5" affiliations: - - name: Unseen Bio ApS, Fruebjergvej 3, 2100 Copenhagen, Denmark + - name: Unseen Bio ApS, Copenhagen, Denmark index: 1 - - name: Microbiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany + - name: Microbiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany index: 2 - - name: Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany + - name: Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany index: 3 - - name: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solnavägen 1, 171 77 Solna, Sweden + - name: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden index: 4 - - name: Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany + - name: Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany index: 5 date: 29 May 2023 bibliography: paper.bib @@ -105,7 +105,7 @@ Assessment tooL (OPAL) [@meyer_assessing_2019] was developed. Creating a community wide assessment faced many of the challenges presented here, however, the chosen solution was to mandate a single output format[^8] for all profilers participating in the challenge. Furthermore, OPAL is an integrated tool -performing assessment and visualization, whereas TAXPASTA follows the UNIX +performing assessment and visualisation, whereas TAXPASTA follows the UNIX philosophy[^9] of doing one thing and doing it well. The BIOM format [@mcdonald_biological_2012] was created with a similar intention of standardising a storage format for microbiome analyses. However, transforming @@ -146,7 +146,7 @@ provided[^10]. For maximum compatibility, TAXPASTA offers a wide range of familiar output file formats, such as text-based, tabular formats (CSV[^1], TSV[^2]), spreadsheets -(ODS[^3], XLSX[^4]), optimized binary formats (Apache Arrow[^5] and +(ODS[^3], XLSX[^4]), optimised binary formats (Apache Arrow[^5] and Parquet[^6]), and the HDF5-based[^7] BIOM format [@mcdonald_biological_2012]. We hope that this will let researchers plug and play TAXPASTA into their existing analysis workflows in a wide range of settings.