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Address editor comments #121

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Jul 8, 2023
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Address editor comments #121

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0f6787c
Simplify affiliations
jfy133 Jul 8, 2023
b8bd8de
Britisch-ize the document
jfy133 Jul 8, 2023
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14 changes: 7 additions & 7 deletions paper/paper.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.
Expand Down