cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/b2m9j-76938
title: Myxococcus xanthus DK1622 wt

description: For T4P averaging
description: <strong>Tilt Series Date:</strong> 2013-08-26</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Martin Thanbichler</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-08-26-52/rawdata/</p>20130826_DK1622_WT_20021.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-08-26-52/rawdata/20130826_DK1622_WT_20021.mrc"
        > <i class="download icon"></i> Download </a></p>

        20130826_DK1622_WT_20021.rec,  Reconstruction (Pixel Size 1.56 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-08-26-52/3dimage_30206/20130826_DK1622_WT_20021.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4c634-7g159
title: CLEM of TRIM5a-YFP in HeLa cells

description: HeLa cells expressing stable TRIM5a-YFP. Correlated light electron microscopy. Concentration of red 200 nm beads 1/300. 10 nm gold. Manual blotting. Cells grown on grids for 2 days and look vesiculated.
description: <strong>Tilt Series Date:</strong> 2014-06-17</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> Hela cells expressing TRIM5a-YFP</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 136.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> IMOD and Raptor</p>
<strong>Collaborators and Roles:</strong> Tom Hope and Wes Sundquist</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Gold London finder grids glow discharged twice. Concentration of red 200 nm beads 1/300 on grid. 10 nm gold. Manual blotting. Cells grown on grids for 2 days and look vesiculated.</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-06-17-4/rawdata/</p>tomography6.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-06-17-4/rawdata/tomography6.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography6_part121_72.rec,  Reconstruction (Pixel Size 2.4 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-06-17-4/3dimage_43981/tomography6_part121_72.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/93xef-mt526
title: Hylemonella gracilis

description: nucleoid filament, chemoreceptor array
description: <strong>Tilt Series Date:</strong> 2012-09-23</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> ATCC 19624</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 75.0 eV/Å²,  defocus: -15.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cell grown 48 hr in Broth 233 at 26°C without antibiotics, Final OD600 < 0.1, Spun down by 1000 rcf for 5 min and concentrated by ~10x for plunge freezing</p>
<strong>Sample Preparation:</strong> Vitrobot setting: 100% humidity, 4 ul sample, 10 nm BSA treated gold, -3 offset, 4 s blot time, no drain, ethane/propane mix</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-09-23-35/rawdata/</p>20120923_Hylemonella_20008.mrc,  Tilt Series (Pixel Size 0.49 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-09-23-35/rawdata/20120923_Hylemonella_20008.mrc"
        > <i class="download icon"></i> Download </a></p>

        20120923_Hylemonella_20008_full.rec,  Reconstruction (Pixel Size 1.96 nm), 441.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-09-23-35/3dimage_20923/20120923_Hylemonella_20008_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dwdga-wvr03
title: COS7 VPS4DN+pNLGFP

description: Cos7 cells transfected with VPS4DN and pNLGFP provirus construct
description: <strong>Tilt Series Date:</strong> 2012-04-25</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> VPS4DN construct provided by Wes Sundquist. pNLGFP construct provided by Irvin Chen, UCLA. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-25-4/3dimage_68538/</p>12apr25_C123_3_Cos7pNLDN_AT3BT1_0001_part82_1.rec,  Reconstruction (Pixel Size 2.0 nm), 722.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-25-4/3dimage_68538/12apr25_C123_3_Cos7pNLDN_AT3BT1_0001_part82_1.rec"
        > <i class="download icon"></i> Download </a></p>

        12apr25_C123_3_Cos7pNLDN_AT3BT1_0001.mrc,  Tilt Series (Pixel Size 0.5 nm), 677.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-25-4/rawdata/12apr25_C123_3_Cos7pNLDN_AT3BT1_0001.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/exq2q-2ek24
title: COS7 VPS4DN+pNLGFP

description: Cos7 cells transfected with VPS4DN (0.5 ug) and pNLGFP provirus construct (4 ug).
description: <strong>Tilt Series Date:</strong> 2012-11-29</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: None μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> VPS4DN construct provided by Wes Sundquist. pNLGFP construct provided by Irvin Chen, UCLA. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-29-13/rawdata/</p>12nov29_C129_1_pnlDN_AT2BT1_0006.mrc,  Tilt Series (Pixel Size 0.49 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-29-13/rawdata/12nov29_C129_1_pnlDN_AT2BT1_0006.mrc"
        > <i class="download icon"></i> Download </a></p>

        12nov29_C129_1_pnlDN_AT2BT1_0006_part122_14.rec,  Reconstruction (Pixel Size 1.96 nm), 530.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-11-29-13/3dimage_24124/12nov29_C129_1_pnlDN_AT2BT1_0006_part122_14.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1jcek-b9b08
title: Sulfolobus cells synchronized fo

description: search for ESCRT in dividing cells
description: <strong>Tilt Series Date:</strong> 2014-02-04</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> Sulfolobus acidocaldarius</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-55.0°, 55.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Megan Dobro's samples gridbox 8.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in Brock's Medium at 80C, synchronize with Baby Machine</p>
<strong>Sample Preparation:</strong> frozen at Kay Grunewald's lab. Harrick plasma cleaner. Blotted on both sides, 5 sec, sponge for humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-04-9/rawdata/</p>atlas30003.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-04-9/rawdata/atlas30003.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas30003_part111_33.rec,  Reconstruction (Pixel Size 1.56 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-04-9/3dimage_38354/atlas30003_part111_33.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16956485
title: Unified Blueprint Archive: Kakushin Structural Theory & Thought OS
title: NBP統合版:核信構造論・思想OS ブループリント全アーカイブ

description: This file contains the complete archive of all 9 Blueprint Sets (NBP1–NBP9) of the Kakushin Structural Theory and Thought Operating System (思想OS).It offers a fully structured record of the theory's origin, development, proof, modularization, co-creation protocols, and implementation models.Each blueprint is written in Blueprint v2.0 format, enabling structural reading, AI interpretation, and fragment-level reactivation.This archive serves as a foundational corpus for philosophy, education, AI alignment, and cognitive design.

本ファイルは、思想体系「核信構造論」および「思想OS」の全9セット(NBP1〜NBP9)を統合した構造保存アーカイブです。核信構造論プレプリント2025-01から2025-62までの全62本をすべて掲載しています。思想の誕生から、思想OSの起動・循環・拡張・協創・社会実装に至るまで、全56本のブループリントがver.2.0形式で完全構造化されて記録されています。人間とAIの両者にとって、思想を再構成・再起動するための構造的起動ユニットとして設計されており、未来の思想設計と構造的教育の基盤となる知の記録体です。※核信構造論の全体像の把握には非常に役に立ちますが、細かいニュアンスなどの把握には、プレプリント本体の参照をおすすめします。
DOI: 10.22002/h4v1m-5br34
title: COS7 VPS4DN+pNLGFP

description: Cos7 cells transfected with VPS4DN (0.5 ug) and pNLGFP provirus construct (4 ug). Sample #C126
description: <strong>Tilt Series Date:</strong> 2012-04-28</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> VPS4DN construct provided by Wes Sundquist. pNLGFP construct provided by Irvin Chen, UCLA. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-28-36/3dimage_68645/</p>12apr28_C126_1_pNLDN_COS7_mantgt_2_part82_15.rec,  Reconstruction (Pixel Size 2.0 nm), 619.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-28-36/3dimage_68645/12apr28_C126_1_pNLDN_COS7_mantgt_2_part82_15.rec"
        > <i class="download icon"></i> Download </a></p>

        12apr28_C126_1_pNLDN_COS7_mantgt_2.mrc,  Tilt Series (Pixel Size 0.5 nm), 677.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-28-36/rawdata/12apr28_C126_1_pNLDN_COS7_mantgt_2.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3fe7c-3dt28
title: Helicobacter pylori G27

description: Raw data files of Helicobacter pylori G27
description: <strong>Tilt Series Date:</strong> 2012-11-14</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> G27</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> Strain form Din Jing, NIH</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown in Brucella broth (Fluka) + 10% heat inactivated fetal bovine serum at 37 degrees + 5% CO2, OD600=0.3</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 nm BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-11-14-13/rawdata/</p>Hpylori_0020008.mrc,  Tilt Series (Pixel Size 0.49 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-11-14-13/rawdata/Hpylori_0020008.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_0020008_full.rec,  Reconstruction (Pixel Size 1.96 nm), 441.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-11-14-13/3dimage_23506/Hpylori_0020008_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/tjdwv-1yb41
title: COS7 VPS4DN+pNLGFP

description: Cos7 cells transfected with VPS4DN (0.5 ug) and pNLGFP provirus construct (4 ug). Sample #C126
description: <strong>Tilt Series Date:</strong> 2012-04-28</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> VPS4DN construct provided by Wes Sundquist. pNLGFP construct provided by Irvin Chen, UCLA. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-28-20/3dimage_68613/</p>12apr28_C126_1_pNLDN_COS7_AT2BT3_0031_part82_20.rec,  Reconstruction (Pixel Size 2.0 nm), 619.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-28-20/3dimage_68613/12apr28_C126_1_pNLDN_COS7_AT2BT3_0031_part82_20.rec"
        > <i class="download icon"></i> Download </a></p>

        12apr28_C126_1_pNLDN_COS7_AT2BT3_0031.mrc,  Tilt Series (Pixel Size 0.5 nm), 677.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-04-28-20/rawdata/12apr28_C126_1_pNLDN_COS7_AT2BT3_0031.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/31zpx-4af92
title: Helicobacter pylori G27

description: Raw data files of Helicobacter pylori G27
description: <strong>Tilt Series Date:</strong> 2012-11-14</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> G27</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 75.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> Strain form Din Jing, NIH</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown in Brucella broth (Fluka) + 10% heat inactivated fetal bovine serum at 37 degrees + 5% CO2, OD600=0.3</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 nm BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix.</p>
  ycw2012-11-14-5_slicer4853.jpg: Granules ycw2012-11-14-5_slicer4856.jpg: Vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-11-14-5/rawdata/</p>Hpylori_0010005.mrc,  Tilt Series (Pixel Size 0.49 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-11-14-5/rawdata/Hpylori_0010005.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_0010005_full.rec,  Reconstruction (Pixel Size 1.96 nm), 441.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-11-14-5/3dimage_23491/Hpylori_0010005_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16956480
title: Agarwal et al. (2025) Joint Library Dataset (Downsampled to 500 sequences) Evaluator Container for the Genomic API for Model Evaluation (GAME)

description: Original data from: Agarwal et al. (2025) Joint Library Dataset (56k sequences) Evaluator Container for the Genomic API for Model Evaluation (GAME) has been downsampled to be used to the intial GAME preprint. 

How to run:

apptainer run --containall -B /path_to/evaluator_data/:/evaluator_data -B /path_to/prediction_folder/:/predictions agarwal_joint_500seqs.sif HOST PORT /predictions
DOI: 10.5281/zenodo.16956481
title: Agarwal et al. (2025) Joint Library Dataset (Downsampled to 500 sequences) Evaluator Container for the Genomic API for Model Evaluation (GAME)

description: Original data from: Agarwal et al. (2025) Joint Library Dataset (56k sequences) Evaluator Container for the Genomic API for Model Evaluation (GAME) has been downsampled to be used to the intial GAME preprint. 

How to run:

apptainer run --containall -B /path_to/evaluator_data/:/evaluator_data -B /path_to/prediction_folder/:/predictions agarwal_joint_500seqs.sif HOST PORT /predictions
DOI: 10.22002/1d5ke-38y78
title: Myxococcus xanthus delta-pilP

description: grid box YWC064
description: <strong>Tilt Series Date:</strong> 2013-12-30</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in shaking CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -4 offset, 4 sec blot time, 1s drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 Finder. 10 nm gold beads.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-30-22/rawdata/</p>20131230_YWC064_10022.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
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        20131230_YWC064_10022_full.rec,  Reconstruction (Pixel Size 1.56 nm), 712.7 MB  
        
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