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Dataset
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update: {"publication_state"=>["version candidate under curator review", "released"], "release_date"=>[nil, Mon, 21 Apr 2025]}
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2025-04-21T19:15:46Z
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Dataset
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update: {"description"=>["#Overview\r\nThese are reference packages for the TIPP3 software for abundance profiling and/or species detection from metagenomic reads (e.g., Illumina, PacBio, Nanopore, etc.). Different refpkg versions are listed.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\n#Changelog\r\nV1.2 (`tipp3-refpkg-1-2.zip`)\r\n 1. Fixed old typos in the file mapping text.\r\n 2. Added new files `taxonomy/species_to_marker.tsv` for new function `run_tipp3.py detection [...parameters]`. Please use the latest release of the TIPP3 software for this new function.\r\nV1 (`tipp3-refpkg.zip`)\r\n 1. Initial release of the TIPP3 reference package.\r\n\r\n#Usage\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `run_tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`", "#Overview\r\nThese are reference packages for the TIPP3 software for abundance profiling and/or species detection from metagenomic reads (e.g., Illumina, PacBio, Nanopore, etc.). Different refpkg versions are listed.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\n#Changelog\r\nV1.2 (`tipp3-refpkg-1-2.zip`)\r\n>>Fixed old typos in the file mapping text.\r\n>>Added new files `taxonomy/species_to_marker.tsv` for new function `run_tipp3.py detection [...parameters]`. Please use the latest release of the TIPP3 software for this new function.\r\nV1 (`tipp3-refpkg.zip`)\r\n>>Initial release of the TIPP3 reference package.\r\n\r\n#Usage\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `run_tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`"]}
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2025-04-21T19:15:31Z
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Dataset
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update: {"description"=>["#Overview\r\nThese are reference packages for the TIPP3 software for abundance profiling and/or species detection from metagenomic reads (e.g., Illumina, PacBio, Nanopore, etc.). Different refpkg versions are listed.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\n#Changelog\r\nV1.2 (`tipp3-refpkg-1-2.zip`)\r\nV1 (`tipp3-refpkg.zip`)\r\n\r\n#Usage\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`", "#Overview\r\nThese are reference packages for the TIPP3 software for abundance profiling and/or species detection from metagenomic reads (e.g., Illumina, PacBio, Nanopore, etc.). Different refpkg versions are listed.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\n#Changelog\r\nV1.2 (`tipp3-refpkg-1-2.zip`)\r\n 1. Fixed old typos in the file mapping text.\r\n 2. Added new files `taxonomy/species_to_marker.tsv` for new function `run_tipp3.py detection [...parameters]`. Please use the latest release of the TIPP3 software for this new function.\r\nV1 (`tipp3-refpkg.zip`)\r\n 1. Initial release of the TIPP3 reference package.\r\n\r\n#Usage\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `run_tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`"]}
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2025-04-21T19:15:00Z
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Dataset
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update: {"description"=>["These are reference packages for the TIPP3 software for abundance profiling and/or species detection from metagenomic reads (e.g., Illumina, PacBio, Nanopore, etc.). Different refpkg versions are listed.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\nUsage:\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`", "#Overview\r\nThese are reference packages for the TIPP3 software for abundance profiling and/or species detection from metagenomic reads (e.g., Illumina, PacBio, Nanopore, etc.). Different refpkg versions are listed.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\n#Changelog\r\nV1.2 (`tipp3-refpkg-1-2.zip`)\r\nV1 (`tipp3-refpkg.zip`)\r\n\r\n#Usage\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`"]}
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2025-04-21T19:12:01Z
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Dataset
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update: {"description"=>["This is a reference package to be used with the TIPP3 software for abundance profiling of metagenomic reads sampled from a microbial community.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\nUsage:\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`", "These are reference packages for the TIPP3 software for abundance profiling and/or species detection from metagenomic reads (e.g., Illumina, PacBio, Nanopore, etc.). Different refpkg versions are listed.\r\nTIPP3 software: https://github.com/c5shen/TIPP3\r\n\r\nUsage:\r\n1. unzip the file to a local directory (will get a folder named \"tipp3-refpkg\").\r\n2. use with TIPP3 software: `tipp3.py -r [path/to/tipp3-refpkg] [other parameters]`"]}
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2025-04-17T15:21:44Z
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Dataset
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update: {"publisher"=>["University of Illinois at Urbana-Champaign", "University of Illinois Urbana-Champaign"]}
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2025-04-17T15:19:36Z
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Dataset
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update: {"hold_state"=>["version candidate under curator review", "none"]}
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2025-04-17T15:06:43Z
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Dataset
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update: {"version_comment"=>[nil, "Fixed old typos in the file mapping txt, and added a new file for new functions of the relevant software TIPP3."]}
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2025-04-17T15:04:23Z
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RelatedMaterial
|
create: {"material_type"=>"Dataset", "availability"=>nil, "link"=>"https://doi.org/10.13012/B2IDB-4931852_V1", "uri"=>"10.13012/B2IDB-4931852_V1", "uri_type"=>"DOI", "citation"=>"Shen, Chengze; Wedell, Eleanor; Warnow, Tandy (2024): TIPP3 Reference Package for Abundance Profiling. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4931852_V1", "dataset_id"=>2939, "selected_type"=>"Dataset", "datacite_list"=>"IsNewVersionOf", "note"=>nil, "feature"=>nil}
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2025-04-17T15:03:41Z
|
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RelatedMaterial
|
create: {"material_type"=>"Code", "availability"=>nil, "link"=>"https://github.com/c5shen/TIPP3", "uri"=>"https://github.com/c5shen/TIPP3", "uri_type"=>"URL", "citation"=>"TIPP3 software", "dataset_id"=>2939, "selected_type"=>"Code", "datacite_list"=>"IsSupplementTo", "note"=>"", "feature"=>nil}
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2025-04-17T15:03:40Z
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Funder
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create: {"name"=>"U.S. National Science Foundation (NSF)", "identifier"=>"10.13039/100000001", "identifier_scheme"=>"DOI", "grant"=>"2006069", "dataset_id"=>2939, "code"=>"NSF"}
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2025-04-17T15:03:40Z
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Creator
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create: {"family_name"=>"Warnow", "given_name"=>"Tandy", "identifier"=>"0000-0001-7717-3514", "email"=>"warnow@illinois.edu", "is_contact"=>false, "row_position"=>3}
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2025-04-17T15:03:40Z
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Creator
|
create: {"family_name"=>"Wedell", "given_name"=>"Eleanor", "identifier"=>"0000-0002-7911-9156", "email"=>"ewedell2@illinois.edu", "is_contact"=>false, "row_position"=>2}
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2025-04-17T15:03:40Z
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Creator
|
create: {"family_name"=>"Shen", "given_name"=>"Chengze", "identifier"=>"0000-0003-2276-9892", "email"=>"chengze5@illinois.edu", "is_contact"=>true, "row_position"=>1}
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2025-04-17T15:03:40Z
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Dataset
|
update: {"corresponding_creator_name"=>[nil, "Chengze Shen"], "corresponding_creator_email"=>[nil, "chengze5@illinois.edu"]}
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2025-04-17T15:03:40Z
|
