cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/feavv-gw488
title: Campylobacter jejuni

description: Session notes: Auto-reconstruct 0.28, 0.025; auto-erase golds; SIRT reconstruction Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-04-21</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-04-21-2_slicer10425.jpg: tube, Campylobacter jejuni
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-04-21-2/rawdata/</p>12apr21a_pflA_0012.st,  Tilt Series (Pixel Size 0.774 nm), 718.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12apr21a_pflA_0012.rec,  Reconstruction (Pixel Size 1.56 nm), 85.2 MB  
        
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DOI: 10.22002/7x2n0-y2e49
title: Campylobacter jejuni

description: Session notes: Titan Krios dataset Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-08-29</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-08-29-19_slicer4876.jpg: non-centered peptidoglycan .  granules mba2012-08-29-19_slicer4878.jpg: Chemoreceptors
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-08-29-19/3dimage_23187/</p>CJejuni_Tomo_33.rec,  Reconstruction (Pixel Size 0.5797 nm), 166.3 MB  
        
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        CJejuni_Tomo_33.st,  Tilt Series (Pixel Size 0.512 nm), 1.1 GB  
        
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DOI: 10.21949/1502562
title: REPURPOSE ME
DOI: 10.15468/dl.qvg2yr
title: Occurrence Download

description: A dataset containing 23517 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Cenchrus clandestinus"
 ]
}

 The dataset includes 23517 records from 231 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046668-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/9ppzt-qwv72
title: Project: peptidoglycan

description: Session notes: First round of data collection on intact sacculi Tilt series notes: notes Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2008-12-05</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 6.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2008-12-05-10/rawdata/</p>08dec05a_grid1_001.mrc,  Tilt Series (Pixel Size 0.782 nm), 1.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        08dec05a_grid1_001_ETOMO_3_13.rec,  Reconstruction (Pixel Size 0.782 nm), 546.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ezw0m-bd462
title: Bacillus subtilis

description: Session notes: Bacillus subtilis 168 cryosections, nominally 70nm thick. Tilt series notes: Cross-section through a cell pole. Tomogram notes: Not much contrast visible.
description: <strong>Tilt Series Date:</strong> 2010-08-28</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-59.0°, 64.0°), step: 0.8°, constant angular increment, dosage: 60.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-08-28-3/rawdata/</p>10aug28b_PGcryo_021.st,  Tilt Series (Pixel Size 0.512 nm), 1.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10aug28b_PGcryo_021.rec,  Reconstruction (Pixel Size 1.024 nm), 190.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/v644h-jzr54
title: Salmonella typhimurium

description: Session notes: Salmonella minicells for fliL flagella, and T3SS. Auto-reconstructed to pixel size 5.18, then binned 2x further, low-pass filtered 0.33, 0.025; gold beads detected 24pix, erased 34pix. Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-03-20</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-03-20-6_slicer5434.jpg: Secretion system
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-03-20-6/rawdata/</p>12mar20b_fliL_0013.st,  Tilt Series (Pixel Size 20.136 nm), 743.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12mar20b_fliL_0013.rec,  Reconstruction (Pixel Size 1.036 nm), 18.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16949861
title: Google Summer of Code 2025 - MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens (Validation release)
DOI: 10.22002/v7gxx-3sz09
title: Salmonella typhimurium

description: Session notes: Salmonella minicells for fliL flagella, and T3SS. Auto-reconstructed to pixel size 5.18, then binned 2x further, low-pass filtered 0.33, 0.025; gold beads detected 24pix, erased 34pix. Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-03-20</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-03-20-10_slicer5459.jpg: Chemoreceptor mba2012-03-20-10_slicer5460.jpg: Unknown
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-03-20-10/rawdata/</p>12mar20b_fliL_0028.st,  Tilt Series (Pixel Size 20.136 nm), 743.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12mar20b_fliL_0028.rec,  Reconstruction (Pixel Size 1.036 nm), 86.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qcca4-q7x45
title: Bacillus subtilis

description: Session notes: Bacillus subtilis PG&TA sacculi, 15 minute achromopeptidase digest Tilt series notes: Partially digested septal peptidoglycan Tomogram notes: Semi-digested sacculus. Seems to be of very high quality. Low contrast nonetheless. Interesting pellets in the pole of one sacculus. Possible tears visible in top right sacculus?
description: <strong>Tilt Series Date:</strong> 2010-09-25</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 66.0°), step: 0.8°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-09-25-1/rawdata/</p>10sep25c_BS_PGTA_15min_001.st,  Tilt Series (Pixel Size 0.774 nm), 2.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10sep25c_BS_PGTA_15min_001.rec,  Reconstruction (Pixel Size 1.548 nm), 252.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xk5z3-stm59
title: Bacillus subtilis

description: Session notes: L-forms of Bacillus subtilis 168 from plate #1 Tilt series notes: Medium-sized L-form in a grid hole. Tomogram notes: L-form with some internal vesicles, one with ribosomes (almost looks like a carboxysome).
description: <strong>Tilt Series Date:</strong> 2010-09-26</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 66.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-09-26-4/rawdata/</p>10sep26a_Lform1_004.st,  Tilt Series (Pixel Size 0.95 nm), 2.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10sep26a_Lform1_004.rec,  Reconstruction (Pixel Size 1.9 nm), 206.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/mjmna-m3k38
title: Campylobacter jejuni

description: Session notes: Medium magnification tomograms of fliI knockout Campylobacter cells Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-04-12</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2011-04-12-23_slicer9411.jpg: filament bundle, Campylobacter jejuni
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-04-12-23/rawdata/</p>11apr12a_fliI_014.st,  Tilt Series (Pixel Size 0.774 nm), 738.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11apr12a_fliI_014.rec,  Reconstruction (Pixel Size 1.548 nm), 35.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.2te3pu
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhodeus amarus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 23 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046583-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/2qvkv-v1z34
title: Campylobacter jejuni

description: Session notes: Campy motB mutant, filtered 0.28, 0.02 after binning 2x more (to ~5.5nm resolution) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-01-13</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-01-13-33_slicer10444.jpg: Campylobacter jejuni .  flagellar motor
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-01-13-33/rawdata/</p>12jan13a_motB_0037.st,  Tilt Series (Pixel Size 0.774 nm), 743.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12jan13a_motB_0037.rec,  Reconstruction (Pixel Size 1.56 nm), 24.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/yz06q-n4702
title: Salmonella typhimurium

description: Session notes: Salmonella fliL minicells with T3SS Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-09-19</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: -1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2012-09-19-18_slicer4484.jpg: Flagella and flagella motor mba2012-09-19-18_slicer4486.jpg: Flagella
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-09-19-18/rawdata/</p>12sep19a_fliL_0027.st,  Tilt Series (Pixel Size 0.512 nm), 636.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        12sep19a_fliL_0027.rec,  Reconstruction (Pixel Size 1.12 nm), 353.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qbdz2-nx970
title: Vibrio fischeri

description: Session notes: Vibrio fischeri WT flagella, binned 4x total then filtered 0.28 (= 4.6nm resolution cutoff) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-12-17</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Vibrio fischeri</p>
<strong>Strain:</strong> ES114</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: 10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2011-12-17-20_slicer6350.jpg: Flagella motor
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-12-17-20/rawdata/</p>11dec17c_WTVFischeri_0006.st,  Tilt Series (Pixel Size 0.632 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11dec17c_WTVFischeri_0006.rec,  Reconstruction (Pixel Size 0.644 nm), 181.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/enpgd-69683
title: Bacillus subtilis

description: Session notes: Bacillus subtilis protoplasts formed by lysozyme addition Tilt series notes: Bacillus subtilis protoplast. Flagella visible. May be lysed? Tomogram notes: Not-very-happy protoplast. DNA can be seen, flagella and motors, plus some intriguing large helical structures...
description: <strong>Tilt Series Date:</strong> 2010-08-30</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-59.0°, 64.0°), step: 1°, constant angular increment, dosage: 60.0 eV/Å²,  defocus: 12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-08-30-2/rawdata/</p>10aug30d_Bsubtilis_proto_002.st,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        10aug30d_Bsubtilis_proto_002.rec,  Reconstruction (Pixel Size 1.9 nm), 188.7 MB  
        
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DOI: 10.22008/fk2/zkjpl6/sdjltw
title: DK6_recharge_1989_2024.7z.003

description: Part3
DK6_HIP_100m_running_2DUZ_AllCells.dfs2
DOI: 10.22008/fk2/zkjpl6/5126r2
title: DK6_recharge_1989_2024.7z.006

description: Part6 DK6_HIP_100m_running_2DUZ_AllCells.dfs2
DOI: 10.22008/fk2/zkjpl6/ew5xwv
title: DK6_recharge_1989_2024.7z.002

description: Part2 DK6_HIP_100m_running_2DUZ_AllCells.dfs2
DOI: 10.22008/fk2/zkjpl6/qjv9ef
title: DK6_recharge_1989_2024.7z.005

description: Part5 DK6_HIP_100m_running_2DUZ_AllCells.dfs2
DOI: 10.22008/fk2/zkjpl6/zrwyyn
title: DK6_recharge_1989_2024.7z.001

description: Part1 DK6_HIP_100m_running_2DUZ_AllCells.dfs2
DOI: 10.22008/fk2/zkjpl6
title: DK6

description: The .zip files contains simulated recharge from DK-model HIP 100m, as the MIKE SHE resultfile: .._2DUZ_AllCells.dfs2, with daily timestep, unit mm/day, for the period 1989 – 2024. Large files (&gt;16GB) are packed with 7-zip into several .zip file, please unpack them using 7-zip in order to get the singe .dfs2 file.
DOI: 10.22008/fk2/zkjpl6/i5gqz4
title: DK6_recharge_1989_2024.7z.004

description: Part4 DK6_HIP_100m_running_2DUZ_AllCells.dfs2