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Input data for the figures of “The cost-benefit trade-off of peritrichous flagellation in bacteria”
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The input data behind every figure of the manuscript “The cost-benefit trade-off of peritrichous flagellation in bacteria” (Giralt-Zúñiga et al.). Download this record, unzip it at the root of a clone of the analysis code, and the figure panels rebuild. Contents. One zip archive with three trees, 256 files and 145.6 MB uncompressed: data/external/ — 39 files. Collaborator deliveries: the promoter-series proteomics tables and the cell-economy model results. data/processed/ — 83 files. Processed measurement tables. Most panel producers read from here. data/source_data/ — 134 files. The registered per-panel source tables, one directory per figure. The archive also carries README.txt and CHECKSUMS.tsv. CHECKSUMS.tsv lists every file with its size and its sha256. How to use it. Clone https://github.com/SalmoLab/salmonella-flagella-cost-benefit at tag v1.0.1, unzip this archive at the repository root, then run make bootstrap and make reproduce-available. 55 of the 60 panels have a registered source and rebuild from these tables. Five image panels have no registered source asset and render a labelled placeholder; the repository README names them. This is a stated limit of the collection. What these tables are. They are not raw instrument output. They are the registered starting points of the panel producers, recorded one by one in config/artifacts.csv of the code release, each with its sha256. Raw mass-spectrometry files are deposited separately in ProteomeXchange through PRIDE. Raw microscopy and tracking files are not part of this collection, and each affected provenance document says so. Overlap with the trajectory record. data/source_data/supplementary_04/ holds the six simulated-trajectory tables of Supplementary Figure 4. The separate record “Simulated trajectories of Supplementary Figure 4” holds the same six files, byte for byte, with the seeds and the regeneration command of each one. This archive keeps them so that it rebuilds every available panel on its own. You need only one of the two downloads. Archive checksum. flagella_cost_benefit_data_v1.0.1.zip, 60,019,103 bytes, sha256 36ce11f054c172a4a38ed0c9b9ef4988c73bce41a0c6ca4418b956d927eb6a13. The archive is byte-reproducible: make data-deposits in the code release rebuilds it with the same checksum. Licence. CC-BY-4.0, with one exception: data/external/cell_economy_results/ (28 files) keeps GPL-3.0-only, the licence of the cell-economy models package it came from (M. Jahn). The full GPL-3.0 text ships with the code release. LICENSES.md in the code repository holds the per-directory map and is the authority. The analysis code is a separate record under GPL-3.0-only.