cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.5gfj9s
title: Occurrence Download

description: A dataset containing 500 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caragana korshinskii",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 500 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015917-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2m6k7r
title: Occurrence Download

description: A dataset containing 3352482 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cerastium glomeratum, Chenopodiastrum hybridum, Clematis terniflora, Coccinia grandis, Crassocephalum rubens, Cuphea carthagenensis, Cuscuta approximata, Cuscuta epilinum, Dioscorea oppositifolia, Elaeagnus pungens, Erechtites valerianifolius, Erigeron philadelphicus, Erigeron glabellus, Euonymus alatus, Euonymus fortunei, Euphorbia dentata, Euphorbia maculata, Evolvulus nummularius, Ficus punctata, Herissantia crispa, Hexasepalum teres, Hydrocotyle verticillata, Ipomoea hederacea, Ipomoea lacunosa, Ipomoea mauritiana, Ipomoea triloba, Jacquemontia tamnifolia, Leucanthemum vulgare, Lolium persicum, Lonicera maackii, Mecardonia procumbens, Melastoma malabathricum, Microstegium vimineum, Mimosa bimucronata, Miscanthus sinensis, Ochrosia elliptica, Oenothera curtiflora, Phelipanche mutelii, Panicum dichotomiflorum, Paspalum conjugatum, Setaria parviflora, Physalis lagascae, Pluchea sagittalis, Porophyllum ruderale, Portulaca pilosa, Praxelis clematidea, Prunus campanulata, Pseudelephantopus spicatus, Pyrus calleryana, Ranunculus arvensis, Ranunculus muricatus, Rhodomyrtus tomentosa, Sorghum nitidum, Sesbania herbacea, Smallanthus uvedalia, Solidago canadensis, Soliva anthemifolia, Sonneratia apetala, Spermacoce alata, Spiraea japonica, Sporobolus alterniflorus, Sporobolus anglicus, Trachycarpus fortunei, Triodanis perfoliata, Othonna othonnites, Veronica arvensis, Veronica hederifolia, Veronica peregrina, Veronica polita, Voacanga africana, Xanthium strumarium, Zephyranthes carinata, Zizania latifolia, Zostera japonica, Zostera marina, Opuntia phaeacantha, Perilla frutescens, Pleioblastus argenteostriatus, Pleioblastus distichus, Pseudosasa humilis, Potamogeton crispus, Rhododendron ponticum, Senegalia asak, Alternanthera paronychioides, Alternanthera spinosa, Aristea ecklonii, Blumea obliqua, Calceolaria mexicana, Cardamine trichocarpa, Carduus nutans, Centaurea iberica, Centratherum punctatum, Centrosema molle, Chamaecrista rotundifolia, Chenopodiastrum murale, Cissampelos pareira, Aegiphila ulei, Corchorus fascicularis)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3352482 records from 5856 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015905-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4q6peu
title: Occurrence Download

description: A dataset containing 1604481 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Rotherham Biological Records Centre - Non-sensitive Records from all taxonomic groups"
 ]
}

 The dataset includes 1604481 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011311-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28847570
title: Analysis code to accompany the manuscript "Climate and species traits shape alpine plant responses to climate change in the U.S. Rocky Mountains"

description: Model selection code for the manuscript "Climate and species traits shape alpine plant responses to climate change in the U.S. Rocky Mountains"
DOI: 10.22002/tyfvh-bxx63
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-96/rawdata/</p>Ecoli_CONjugation56.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-96/rawdata/Ecoli_CONjugation56.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation56_part101_25.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-96/3dimage_107190/Ecoli_CONjugation56_part101_25.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation56.mrc.mdoc,  51.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-96/rawdata/Ecoli_CONjugation56.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7r85c-ycc77
title: EPEC_8770_U2OS

description: EPEC cells strain 8770 incubated with U2OS. The aim is to see bacterial nanotubes connected  .  to the eukaryotic cell.
description: <strong>Tilt Series Date:</strong> 2020-02-14</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8770, EPEC 8612 + Δbfp ΔtraD-ygeB ΔfinO-traI</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The strain EPEC 8770 is obtained from Ritesh (Ilan Rosenshine lab, the Hebrew university) and . Amit (Sigal ben Yehuda lab). U2OS was obtained from Wei Zhao in the Jensen lab.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> U2OS were grown on gold finders grids overnight in DMEM medium at 37 C. next day the . grids were washed with PBS and incubated with DMEM+FCS and bacteria were added (1:100) . and the grids were cultured for 3.5 hours at 37C. Then the grids were washed twice with PBS . and incubated with starvation buffer for 1 hour. The samples were plunge frozen.</p>
<strong>Sample Preparation:</strong> Samples were blotted manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-14-4/rawdata/</p>EPEC_U2OS_tilt6.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-14-4/rawdata/EPEC_U2OS_tilt6.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_U2OS_tilt6_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-14-4/3dimage_111034/EPEC_U2OS_tilt6_full.rec"
        > <i class="download icon"></i> Download </a></p>

        EPEC_U2OS_tilt6.mrc.mdoc,  34.4 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-14-4/rawdata/EPEC_U2OS_tilt6.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4wscq-r8k32
title: BacillusSubtilis_328_4hr

description: This is Bacillus Subtilis tomograms PonA mutant strain 328 (obtained from Amit in Sigal Ben  .  Yehuda lab at the Hebrew university). The idea is to image bacterial nanotubes in Bacilus .  Subtilis.
description: <strong>Tilt Series Date:</strong> 2020-02-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> AB328, ΔponA ΔymdB amyE::ymdB Δhag</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The samples were prepared with Amit and Ritesh (from Sigal Ben Yehuda and Ilan Rosenshine . labs at the Hebrew University). These Samples were incubated for four hours on grids on plates . (I will write the details on my Labjournal).  </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Samples were grown on the grids on agar plates for four hours. Detailed description is in the lab . journal. Yuxi helped in the sample preparation and data collection.</p>
<strong>Sample Preparation:</strong> Samples were taken from the agar plates and washed few times in PBS. Then they were blotted . and plunge-frozen.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-14/rawdata/</p>Bsubtilis_328_4hr_conventional9.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-14/rawdata/Bsubtilis_328_4hr_conventional9.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bsubtilis_328_4hr_conventional9_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-14/3dimage_110660/Bsubtilis_328_4hr_conventional9_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Bsubtilis_328_4hr_conventional9.mrc.mdoc,  23.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-14/rawdata/Bsubtilis_328_4hr_conventional9.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/k5x5a-hqf18
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-101/rawdata/</p>Ecoli_CONjugation60.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-101/rawdata/Ecoli_CONjugation60.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation60_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-101/3dimage_107202/Ecoli_CONjugation60_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation60.mrc.mdoc,  50.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-101/rawdata/Ecoli_CONjugation60.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/kzgwg-vh836
title: BacillusSubtilis_328_4hr

description: This is Bacillus Subtilis tomograms PonA mutant strain 328 (obtained from Amit in Sigal Ben  .  Yehuda lab at the Hebrew university). The idea is to image bacterial nanotubes in Bacilus .  Subtilis.
description: <strong>Tilt Series Date:</strong> 2020-02-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> AB328, ΔponA ΔymdB amyE::ymdB Δhag</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The samples were prepared with Amit and Ritesh (from Sigal Ben Yehuda and Ilan Rosenshine . labs at the Hebrew University). These Samples were incubated for four hours on grids on plates . (I will write the details on my Labjournal).  </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Samples were grown on the grids on agar plates for four hours. Detailed description is in the lab . journal. Yuxi helped in the sample preparation and data collection.</p>
<strong>Sample Preparation:</strong> Samples were taken from the agar plates and washed few times in PBS. Then they were blotted . and plunge-frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-9/rawdata/</p>testTilt.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-9/rawdata/testTilt.mrc"
        > <i class="download icon"></i> Download </a></p>

        testTilt_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-9/3dimage_110656/testTilt_full.rec"
        > <i class="download icon"></i> Download </a></p>

        testTilt.mrc.mdoc,  23.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-9/rawdata/testTilt.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.60732/4221d2fa
title: OC20_S2EF_val_ood_cat

description: OC20_S2EF_val_ood_cat is the out-of-domain validation set of the OC20 Structure to Energy and Forces (S2EF) dataset featuring unseen catalyst composition. Features include energy, atomic forces and data from the OC20 mappings file, including adsorbate id, materials project bulk id and miller index.
DOI: 10.60732/f8398b5c
title: OC20_S2EF_val_ood_both

description: OC20_S2EF_val_ood_both is the out-of-domain validation set of the OC20 Structure to Energy and Forces (S2EF) dataset featuring both unseen catalyst composition and unseen adsorbate. Features include energy, atomic forces and data from the OC20 mappings file, including adsorbate id, materials project bulk id and miller index.
DOI: 10.60732/d820e77c
title: OC20_S2EF_val_ood_ads

description: OC20_S2EF_val_ood_ads is the out-of-domain validation set of the OC20 Structure to Energy and Forces (S2EF) dataset featuring unseen adsorbate. Features include energy, atomic forces and data from the OC20 mappings file, including adsorbate id, materials project bulk id and miller index.
DOI: 10.60732/eaea5062
title: OC20_S2EF_val_id

description: OC20_S2EF_val_id is the ~1-million structure in-domain validation set of the OC20 Structure to Energy and Forces (S2EF) dataset. Features include energy, atomic forces and data from the OC20 mappings file, including adsorbate id, materials project bulk id and miller index.
DOI: 10.60732/672cc613
title: OC20_S2EF_train_2M

description: OC20_S2EF_train_2M is the 2 million structure training subset of the OC20 Structure to Energy and Forces dataset. Features include potential energy, free energy and atomic forces. Data from the OC20 mappings file, including adsorbate id, materials project bulk id, miller index, shift and others.
DOI: 10.60732/6ccdeb1d
title: OC20_S2EF_train_200K

description: OC20_S2EF_train_200K is the 200K training split of the OC20 Structure to Energy and Forces (S2EF) task.
DOI: 10.60732/9f03e9be
title: OC20_S2EF_train_20M

description: OC20_S2EF_train_20M is the 20 million structure training subset of the OC20 Structure to Energy and Forces dataset. Features include potential energy, free energy and atomic forces. Data from the OC20 mappings file, including adsorbate id, materials project bulk id, miller index, shift and others.
DOI: 10.60732/b4005525
title: OC20_IS2RES_val_id

description: OC20_IS2RES_val_id is the in-domain validation set for the OC20 Initial Structure to Relaxed Structure (IS2RS) and Initial Structure to Relaxed Energy (IS2RE) tasks. Features include energy, atomic forces and data from the OC20 mappings file, including adsorbate id, materials project bulk id and miller index.
DOI: 10.60732/0947596b
title: OC20_IS2RES_val_ood_ads

description: OC20_IS2RES_ood_ads is the out-of-domain validation set for the OC20 Initial Structure to Relaxed Structure (IS2RS) and Initial Structure to Relaxed Energy (IS2RE) tasks with unseen adsorbates. Features include energy, atomic forces and data from the OC20 mappings file, including adsorbate id, materials project bulk id and miller index.
DOI: 10.5281/zenodo.15148511
title: Effort-Aware Benchmark Dataset for Sokoban Pathfinding Algorithms

description: This repository provides a comprehensive collection of datasets, pretrained models, solver outputs, and supporting resources focused on the effort-aware evaluation of classical pathfinding algorithms within procedurally generated Sokoban environments.

The datasets capture solver behavior across six dimensions of computational effort — solution steps, cumulative path cost, number of node expansions, number of edge traversals, wall-clock runtime, and peak memory consumption.Evaluated solvers include Breadth-First Search (BFS), Depth-First Search (DFS), A* Search, and Greedy Best-First Search (GBFS), covering a broad spectrum of uninformed and heuristic search strategies.

The repository contents include:





Datasets: CSV files recording solver metrics across Sokoban levels of varying grid sizes (5×5, 6×6, 7×7, and 8×8), including merged datasets and difficulty-labeled datasets using clustering-based classification.




Pretrained Models:





KMeans clustering model trained on normalized effort metrics, uncovering structural patterns among levels.




Min-Max feature scaler used during dimensionality reduction and model training.




Solver-to-cluster mapping artifact supporting adaptive solver selection strategies.






Meta-Solver Predictions: Prediction outputs associating early search features with the solver most likely to succeed on a given level.




Documentation: Detailed README file explaining data schema, model usage, and instructions for reproducing key analyses and visualizations.



Key experimental steps supported by this repository include effort-based clustering of problem instances, evaluation of solver performance trade-offs, identification of structural difficulty patterns in Sokoban levels, and prediction of solver suitability using lightweight effort-aware features. 

This repository supports reproducible research in effort-aware pathfinding, instance-aware algorithm selection, and adaptive planning strategies.It is intended to facilitate future studies in game AI, robotic motion planning, combinatorial search, and hybrid symbolic-learning planning frameworks.

How to Cite This WorkIf you use this dataset, models, or any associated resources in your research, please cite this Zenodo record using the following DOI:10.5281/zenodo.15297570
DOI: 10.5281/zenodo.15148512
title: Effort-Aware Benchmark Dataset for Sokoban Pathfinding Algorithms