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  • Digital Humanities and Cultural Heritage
  • 2019-2023
  • Research data
  • ZENODO
  • Spiral - Imperial College Digital R...
  • Digital Humanities and Cultural Her...
  • NEANIAS Space Research Community

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Dallago, Christian; Marquet, Céline; Rost, Burkhard;

    Residue and sequence embeddings of the fly (drosophila melanogaster) proteome (FlyBase for organism drosophila melanogaster, downloaded on 2022.03.01) computed using bio_embeddings (bioembeddings.com) using the ProtT5 embedder at full precision (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3). To open the embeddings file, please see this notebook. The embeddings will be indexed by numbers according to the mapping file (mapping_file.csv) in this dataset. All following results will share the same mapping (for instance, to access the variation prediction results, by accessing index "0", you will query results for the sequence "FBpp0304622"). Additionally: - Sequence-level predictions of subcellular localization in 10 classes using LA (https://www.biorxiv.org/content/10.1101/2021.04.25.441334v1) - Residue-level three state secondary structure prediction (alpha, sheet or other) using models reported in the ProtTrans paper (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3) - Residue-level prediction of conservation (in 9 states) and of variation effect (from 0 [no-effect] to 1 [effect]) using VESPAl (https://doi.org/10.1007/s00439-021-02411-y) Files included: - dmel-all-translation-r6.44.fasta --> FASTA-formatted sequences of drosophila melanogaster from FlyBase - mapping_file.csv --> A CSV file mapping the identifiers used in the following files (from 0 to 30737) to the identifiers in the FlyBase fasta file (dmel-all-translation-r6.44.fasta). - DSSP3_fly_ProtT5Sec.fasta --> Secondary structure predictions in three states for each residue of each protein in dmel-all-translation-r6.44.fasta. "H" stands for Helix; "E" stands for Sheet; "C" stands for Other. - subcell_fly_LA_ProtT5.csv --> Subcellular location (10 states) and memrane-boundness (2 states) for each protein in dmel-all-translation-r6.44.fasta - embeddings_file.h5 --> per-residue embeddings of sequences in dmel-all-translation-r6.44.fasta. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length Lx1024, with L being the length of the protein sequence. Datasets are indexed using integers. The original sequence identifier (from the FASTA header) can be accessed through the "original_id" attribute. See https://docs.bioembeddings.com/v0.2.0/notebooks/open_embedding_file.html for information on how to open the file. - reduced_embeddings_file.h5 --> per-sequence embeddings of sequences in dmel-all-translation-r6.44.fasta (obtained by mean-pooling the residue-embeddings along the length dimension of the protein sequence). Each dataset in the .h5 file represents a protein sequence and contains a vector of size 1024 (meaning, each sequence has the same dimension). - conspred_probs.h5 --> per-sequence conservation probability (softmax) prediction of sequences in dmel-all-translation-r6.44.fasta in 9 classes. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length 9xL, with L being the length of the protein sequence, and 9 being the predicted conservation class (index 0 = very variable; index 8 = very conserved) - vespal_SAVeffect_fly.zip --> zipped .h5 file of per-sequence variation predictions of sequences in dmel-all-translation-r6.44.fasta on a scale from 0 (neutral) to 1 (effect). -1 indicates WT substitution. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length 20xL, with L being the length of the protein sequence, and 20 being the predicted variation score for each residue substitution (AAs in the following order: "ALGVSREDTIPKFQNYMHWC" . Meaning that index 0 = substitution of the residue to "A", index = 1 substitution to residue "L", aso.)

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    ZENODO
    Dataset . 2022
    Data sources: Datacite
    ZENODO
    Dataset . 2022
    Data sources: ZENODO
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      ZENODO
      Dataset . 2022
      Data sources: Datacite
      ZENODO
      Dataset . 2022
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Divya M. Persaud; Robert Barnes;

    {"references": ["Barnes, R., S. Gupta, C. Traxler, T. Ortner, A. Bauer, G. Hesina, G. Paar, et al. 2018. \"Geological Analysis of Martian Rover-Derived Digital Outcrop Models Using the 3-D Visualization Tool, Planetary Robotics 3-D Viewer\u2014PRo3D.\" Earth and Space Science 5: 1\u201323. https://doi.org/10.1002/2018EA000374.", "Fraeman, A. A., B. L. Ehlmann, R. E. Arvidson, C. S. Edwards, J. P. Grotzinger, R. E. Milliken, D. P. Quinn, and M. S. Rice. 2016. \"The Stratigraphy and Evolution of Lower Mount Sharp from Spectral, Morphological, and Thermophysical Orbital Data Sets.\" Journal of Geophysical Research E: Planets 121 (9): 1713\u201336. https://doi.org/10.1002/2016JE005095.Received.", "Hughes, M. N. 2021. \"Landscape Evolution at Endeavour and Gale Craters on Mars, and How Terrain Characteristics Correlate with Mineralogy on Lower Mount Sharp, Gale Crater.\" https://doi.org/10.7936/c6se-5895.", "Milliken, R. E., J. P. Grotzinger, and B. J. Thomson. 2010. \"Paleoclimate of Mars as Captured by the Stratigraphic Record in Gale Crater.\" Geophysical Research Letters 37 (4): 1\u20136. https://doi.org/10.1029/2009GL041870.", "Persaud, D. M. (2021). Co-registered U. Arizona HiRISE DTM and ORI over Sakarya Vallis, Gale Crater, Mars [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5808371", "Persaud, D. M. (2021). Multi-Resolution Basemap of Northwest Aeolis Mons, Gale Crater, Mars [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5808381", "Thomson, B. J., N. T. Bridges, R. E. Milliken, A. M. Baldridge, S. J. Hook, J. K. Crowley, G. M. Marion, C. R. de Souza Filho, A. J. Brown, and C. M. Weitz. 2011. \"Constraints on the Origin and Evolution of the Layered Mound in Gale Crater, Mars Using Mars Reconnaissance Orbiter Data.\" Icarus 214 (2): 413\u201332. https://doi.org/10.1016/j.icarus.2011.05.002."]} This dataset comprises the unit map derived from 3D analysis of Sakarya Vallis in Gale crater, Mars. The units are named Package 1–7. These packages have been extrapolated from morpho-stratigraphic analysis of a HiRISE scene in PRo3D. They have been further extrapolated using underlying image data. Included here is a shapefile representing the marker bed (Milliken et al. 2010) in Gale crater. The "CDD" refers to the Central Debris Deposit, identified by Hughes (2021). The structural data represents dip measurements along the boundaries of these packages within the feature; the "sub-package" data represent layering within the packages. For more on how dip is calculated in PRo3D, see https://pro3d.space/. Finally, the profiles mark the locations where topographic profiles were extracted for constructing cross-sections, as discussed in the thesis Persaud (2022). These data are intended to be displayed with the HiRISE ORI (https://doi.org/10.5281/zenodo.5808371) and CTX ORI mosaic (https://doi.org/10.5281/zenodo.5808357) over Sakarya Vallis, and over the basemap over the northwest of Aeolis Mons (https://doi.org/10.5281/zenodo.5808381). Format: SHP, SHX, DBF, PRJ, QPJ Projection: Equidistant cylindrical Datum: Spheroid (r = 3396.190 km) N.B. the PROJ4 format of the project is "+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +a=3396190 +b=3396190 +units=m +no_defs" The first author is now at Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California. Contact: divya.m.persaud@jpl.nasa.gov Part of this work was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to NASA. Government sponsorship acknowledged.

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    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: ZENODO
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      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    Test for the TEI Critical Apparatus Toolbox, along with their outcome and summaries. They are related to an article to be published in RIDE 14.

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    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Christian Dallago; Burkhard Rost;

    Residue and sequence embeddings of the human proteome (SwissProt for organism Human, downloaded on 2021.06.09) computed using bio_embeddings (bioembeddings.com) using the ProtT5 embedder at full precision (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3). Additionally: - Sequence-level predictions of subcellular localization in 10 classes using LA (https://www.biorxiv.org/content/10.1101/2021.04.25.441334v1) - Residue-level three state secondary structure prediction (alpha, sheet or other) using models reported in the ProtTrans paper (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3) Files included: - human.fasta --> FASTA-formatted sequences of human from SwissProt - DSSP3_human_ProtT5Sec.fasta --> Secondary structure predictions in three states for each residue of each protein in human.fasta. "H" stands for Helix; "E" stands for Sheet; "C" stands for Other. - subcell_human_LA_ProtT5.csv --> Subcellular location (10 states) and memrane-boundness (2 states) for each protein in human.fasta - embeddings_file.h5 --> per-residue embeddings of sequences in human.fasta. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length Lx1024, with L being the length of the protein sequence. Datasets are indexed using integers. The original sequence identifier (from the FASTA header) can be accessed through the "original_id" attribute. See https://docs.bioembeddings.com/v0.2.0/notebooks/open_embedding_file.html for information on how to open the file - reduced_embeddings_file.h5 --> per-sequence embeddings of sequences in human.fasta (obtained by mean-pooling the residue-embeddings along the length dimension of the protein sequence). Each dataset in the .h5 file represents a protein sequence and contains a vector of size 1024 (meaning, each sequence has the same dimension).

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
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      ZENODO
      Dataset . 2021
      Data sources: Datacite
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
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    Authors: McIlvenny, Paul;

    A dense composite 2D video clip showing the different screens and audio chat of three analysts using CAVA360VR (Collaborate, Annotate, Visualise, Analysis 360 video in Virtual Reality) to hold a live virtual data session at a national research conference in 2019. The three co-analysts (M, J and P) in VR were collaborating even though they were in three different physical locations across two countries. The video data that they analysed together involved multicam recordings of six participants in a two-team competition to solve a Lego puzzle when only one member in each group could view the hidden Lego construction in order to instruct the others in their team how to rebuild it from a pile of blocks. The video clip shows the viewport chosen by each of the three analysts. There are three possible viewports that can be selected: a) what they each see in their VR HMD (head-mounted display), b) an over-the-shoulder view (with an outline showing their avatar), and c) a static third-person view of the three analysts. A fourth screen shows the view of an observer in non-VR mode.

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    ZENODO
    Audiovisual . 2020
    License: CC BY NC ND
    Data sources: Datacite
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    ZENODO
    Audiovisual . 2020
    License: CC BY NC ND
    Data sources: ZENODO
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      ZENODO
      Audiovisual . 2020
      License: CC BY NC ND
      Data sources: Datacite
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      ZENODO
      Audiovisual . 2020
      License: CC BY NC ND
      Data sources: ZENODO
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    Authors: Hodel, Tobias;

    Visualizations produced from networks regarding the production of charters in and for Königsfelden Abbey. A commented version of all networks is added as PDF file: modularity-and-networks.pdf. The referenced numbers of people can be found as PDF file: kf-personenliste.pdf. The data used, is published online: https://doi.org/10.5281/zenodo.632560

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    ZENODO
    Image . 2019
    License: CC BY
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    ZENODO
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    Authors: Pat Scott;

    This is the example MultiNest chain from arXiv:0909.3300, used in the pippi example, and referred to in the pippi paper and documentation. This is the example MultiNest chain from arXiv:0909.3300, used in the pippi example, and referred to in the pippi paper and documentation.

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    ZENODO
    Dataset . 2019
    License: CC BY
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    ZENODO
    Dataset . 2019
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      ZENODO
      Dataset . 2019
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      ZENODO
      Dataset . 2019
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Dallago, Christian; Marquet, Céline; Rost, Burkhard;

    Residue and sequence embeddings of the fly (drosophila melanogaster) proteome (FlyBase for organism drosophila melanogaster, downloaded on 2022.03.01) computed using bio_embeddings (bioembeddings.com) using the ProtT5 embedder at full precision (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3). To open the embeddings file, please see this notebook. The embeddings will be indexed by numbers according to the mapping file (mapping_file.csv) in this dataset. All following results will share the same mapping (for instance, to access the variation prediction results, by accessing index "0", you will query results for the sequence "FBpp0304622"). Additionally: - Sequence-level predictions of subcellular localization in 10 classes using LA (https://www.biorxiv.org/content/10.1101/2021.04.25.441334v1) - Residue-level three state secondary structure prediction (alpha, sheet or other) using models reported in the ProtTrans paper (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3) - Residue-level prediction of conservation (in 9 states) and of variation effect (from 0 [no-effect] to 1 [effect]) using VESPAl (https://doi.org/10.1007/s00439-021-02411-y) Files included: - dmel-all-translation-r6.44.fasta --> FASTA-formatted sequences of drosophila melanogaster from FlyBase - mapping_file.csv --> A CSV file mapping the identifiers used in the following files (from 0 to 30737) to the identifiers in the FlyBase fasta file (dmel-all-translation-r6.44.fasta). - DSSP3_fly_ProtT5Sec.fasta --> Secondary structure predictions in three states for each residue of each protein in dmel-all-translation-r6.44.fasta. "H" stands for Helix; "E" stands for Sheet; "C" stands for Other. - subcell_fly_LA_ProtT5.csv --> Subcellular location (10 states) and memrane-boundness (2 states) for each protein in dmel-all-translation-r6.44.fasta - embeddings_file.h5 --> per-residue embeddings of sequences in dmel-all-translation-r6.44.fasta. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length Lx1024, with L being the length of the protein sequence. Datasets are indexed using integers. The original sequence identifier (from the FASTA header) can be accessed through the "original_id" attribute. See https://docs.bioembeddings.com/v0.2.0/notebooks/open_embedding_file.html for information on how to open the file. - reduced_embeddings_file.h5 --> per-sequence embeddings of sequences in dmel-all-translation-r6.44.fasta (obtained by mean-pooling the residue-embeddings along the length dimension of the protein sequence). Each dataset in the .h5 file represents a protein sequence and contains a vector of size 1024 (meaning, each sequence has the same dimension). - conspred_probs.h5 --> per-sequence conservation probability (softmax) prediction of sequences in dmel-all-translation-r6.44.fasta in 9 classes. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length 9xL, with L being the length of the protein sequence, and 9 being the predicted conservation class (index 0 = very variable; index 8 = very conserved) - vespal_SAVeffect_fly.zip --> zipped .h5 file of per-sequence variation predictions of sequences in dmel-all-translation-r6.44.fasta on a scale from 0 (neutral) to 1 (effect). -1 indicates WT substitution. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length 20xL, with L being the length of the protein sequence, and 20 being the predicted variation score for each residue substitution (AAs in the following order: "ALGVSREDTIPKFQNYMHWC" . Meaning that index 0 = substitution of the residue to "A", index = 1 substitution to residue "L", aso.)

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    ZENODO
    Dataset . 2022
    Data sources: Datacite
    ZENODO
    Dataset . 2022
    Data sources: ZENODO
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      ZENODO
      Dataset . 2022
      Data sources: Datacite
      ZENODO
      Dataset . 2022
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Divya M. Persaud; Robert Barnes;

    {"references": ["Barnes, R., S. Gupta, C. Traxler, T. Ortner, A. Bauer, G. Hesina, G. Paar, et al. 2018. \"Geological Analysis of Martian Rover-Derived Digital Outcrop Models Using the 3-D Visualization Tool, Planetary Robotics 3-D Viewer\u2014PRo3D.\" Earth and Space Science 5: 1\u201323. https://doi.org/10.1002/2018EA000374.", "Fraeman, A. A., B. L. Ehlmann, R. E. Arvidson, C. S. Edwards, J. P. Grotzinger, R. E. Milliken, D. P. Quinn, and M. S. Rice. 2016. \"The Stratigraphy and Evolution of Lower Mount Sharp from Spectral, Morphological, and Thermophysical Orbital Data Sets.\" Journal of Geophysical Research E: Planets 121 (9): 1713\u201336. https://doi.org/10.1002/2016JE005095.Received.", "Hughes, M. N. 2021. \"Landscape Evolution at Endeavour and Gale Craters on Mars, and How Terrain Characteristics Correlate with Mineralogy on Lower Mount Sharp, Gale Crater.\" https://doi.org/10.7936/c6se-5895.", "Milliken, R. E., J. P. Grotzinger, and B. J. Thomson. 2010. \"Paleoclimate of Mars as Captured by the Stratigraphic Record in Gale Crater.\" Geophysical Research Letters 37 (4): 1\u20136. https://doi.org/10.1029/2009GL041870.", "Persaud, D. M. (2021). Co-registered U. Arizona HiRISE DTM and ORI over Sakarya Vallis, Gale Crater, Mars [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5808371", "Persaud, D. M. (2021). Multi-Resolution Basemap of Northwest Aeolis Mons, Gale Crater, Mars [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5808381", "Thomson, B. J., N. T. Bridges, R. E. Milliken, A. M. Baldridge, S. J. Hook, J. K. Crowley, G. M. Marion, C. R. de Souza Filho, A. J. Brown, and C. M. Weitz. 2011. \"Constraints on the Origin and Evolution of the Layered Mound in Gale Crater, Mars Using Mars Reconnaissance Orbiter Data.\" Icarus 214 (2): 413\u201332. https://doi.org/10.1016/j.icarus.2011.05.002."]} This dataset comprises the unit map derived from 3D analysis of Sakarya Vallis in Gale crater, Mars. The units are named Package 1–7. These packages have been extrapolated from morpho-stratigraphic analysis of a HiRISE scene in PRo3D. They have been further extrapolated using underlying image data. Included here is a shapefile representing the marker bed (Milliken et al. 2010) in Gale crater. The "CDD" refers to the Central Debris Deposit, identified by Hughes (2021). The structural data represents dip measurements along the boundaries of these packages within the feature; the "sub-package" data represent layering within the packages. For more on how dip is calculated in PRo3D, see https://pro3d.space/. Finally, the profiles mark the locations where topographic profiles were extracted for constructing cross-sections, as discussed in the thesis Persaud (2022). These data are intended to be displayed with the HiRISE ORI (https://doi.org/10.5281/zenodo.5808371) and CTX ORI mosaic (https://doi.org/10.5281/zenodo.5808357) over Sakarya Vallis, and over the basemap over the northwest of Aeolis Mons (https://doi.org/10.5281/zenodo.5808381). Format: SHP, SHX, DBF, PRJ, QPJ Projection: Equidistant cylindrical Datum: Spheroid (r = 3396.190 km) N.B. the PROJ4 format of the project is "+proj=eqc +lat_ts=0 +lat_0=0 +lon_0=0 +x_0=0 +y_0=0 +a=3396190 +b=3396190 +units=m +no_defs" The first author is now at Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California. Contact: divya.m.persaud@jpl.nasa.gov Part of this work was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to NASA. Government sponsorship acknowledged.

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    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    Test for the TEI Critical Apparatus Toolbox, along with their outcome and summaries. They are related to an article to be published in RIDE 14.

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    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2021
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: ZENODO
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      ZENODO
      Dataset . 2021
      License: CC BY
      Data sources: Datacite
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    Authors: Christian Dallago; Burkhard Rost;

    Residue and sequence embeddings of the human proteome (SwissProt for organism Human, downloaded on 2021.06.09) computed using bio_embeddings (bioembeddings.com) using the ProtT5 embedder at full precision (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3). Additionally: - Sequence-level predictions of subcellular localization in 10 classes using LA (https://www.biorxiv.org/content/10.1101/2021.04.25.441334v1) - Residue-level three state secondary structure prediction (alpha, sheet or other) using models reported in the ProtTrans paper (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3) Files included: - human.fasta --> FASTA-formatted sequences of human from SwissProt - DSSP3_human_ProtT5Sec.fasta --> Secondary structure predictions in three states for each residue of each protein in human.fasta. "H" stands for Helix; "E" stands for Sheet; "C" stands for Other. - subcell_human_LA_ProtT5.csv --> Subcellular location (10 states) and memrane-boundness (2 states) for each protein in human.fasta - embeddings_file.h5 --> per-residue embeddings of sequences in human.fasta. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length Lx1024, with L being the length of the protein sequence. Datasets are indexed using integers. The original sequence identifier (from the FASTA header) can be accessed through the "original_id" attribute. See https://docs.bioembeddings.com/v0.2.0/notebooks/open_embedding_file.html for information on how to open the file - reduced_embeddings_file.h5 --> per-sequence embeddings of sequences in human.fasta (obtained by mean-pooling the residue-embeddings along the length dimension of the protein sequence). Each dataset in the .h5 file represents a protein sequence and contains a vector of size 1024 (meaning, each sequence has the same dimension).

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
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      ZENODO
      Dataset . 2021
      Data sources: Datacite
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
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    Authors: McIlvenny, Paul;

    A dense composite 2D video clip showing the different screens and audio chat of three analysts using CAVA360VR (Collaborate, Annotate, Visualise, Analysis 360 video in Virtual Reality) to hold a live virtual data session at a national research conference in 2019. The three co-analysts (M, J and P) in VR were collaborating even though they were in three different physical locations across two countries. The video data that they analysed together involved multicam recordings of six participants in a two-team competition to solve a Lego puzzle when only one member in each group could view the hidden Lego construction in order to instruct the others in their team how to rebuild it from a pile of blocks. The video clip shows the viewport chosen by each of the three analysts. There are three possible viewports that can be selected: a) what they each see in their VR HMD (head-mounted display), b) an over-the-shoulder view (with an outline showing their avatar), and c) a static third-person view of the three analysts. A fourth screen shows the view of an observer in non-VR mode.

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    ZENODO
    Audiovisual . 2020
    License: CC BY NC ND
    Data sources: Datacite
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Audiovisual . 2020
    License: CC BY NC ND
    Data sources: ZENODO
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Audiovisual . 2020
      License: CC BY NC ND
      Data sources: Datacite
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Audiovisual . 2020
      License: CC BY NC ND
      Data sources: ZENODO
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    Authors: Hodel, Tobias;

    Visualizations produced from networks regarding the production of charters in and for Königsfelden Abbey. A commented version of all networks is added as PDF file: modularity-and-networks.pdf. The referenced numbers of people can be found as PDF file: kf-personenliste.pdf. The data used, is published online: https://doi.org/10.5281/zenodo.632560

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    ZENODO
    Image . 2019
    License: CC BY
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Image . 2019
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Image . 2019
      License: CC BY
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Image . 2019
      License: CC BY
      Data sources: Datacite
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    Authors: Pat Scott;

    This is the example MultiNest chain from arXiv:0909.3300, used in the pippi example, and referred to in the pippi paper and documentation. This is the example MultiNest chain from arXiv:0909.3300, used in the pippi example, and referred to in the pippi paper and documentation.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Spiral - Imperial Co...arrow_drop_down
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    ZENODO
    Dataset . 2019
    License: CC BY
    Data sources: Datacite
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2019
    License: CC BY
    Data sources: ZENODO
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      ZENODO
      Dataset . 2019
      License: CC BY
      Data sources: Datacite
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      ZENODO
      Dataset . 2019
      License: CC BY
      Data sources: ZENODO
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