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  "URL": "https://github.com/noaa-fims/fims, https://noaa-fims.github.io,\nhttps://noaa-fisheries-integrated-toolbox.r-universe.dev/FIMS,\nhttps://noaa-fims.github.io/FIMS",
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  "Date/Publication": "2026-06-08 22:47:11 UTC",
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