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  • Digital Humanities and Cultural Heritage
  • 2017-2021
  • Research software
  • European Commission
  • English

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  • Authors: Joseph Padfield;

    This is an interactive live modelling system which can automatically convert simple tab separated triples or JSON-LD into graphical models using the mermaid library. General updates and improvements have been carried out, with the addition of the Mermaid SubGraph functionality to aid the organisation of more complex models. Instructions: Full details and instructions relating to how this system works is still being developed, however several examples are included in the interactive web site: dynamic modelling, with all of the related code presented in GitHub.

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    Software . 2021
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      Software . 2021
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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: Joseph Padfield;

    This is a simple set of processes for creating a standard set of webpages based on a simple set of json files. This project is intended to work along side other projects to provide a simple way of creating a set of consistent webpages, which can be delivered as part of your own GitHub project using GitHub pages. It has been extended to allow more complex features such as presenting IIIIF (https://iiif.io) viewers, Timelines, and ordered Lists & Galleries. Various updates to the related JavaScript libraries have been added along with an option to use the whole system to create dynamic as well as static websites. For more detail and the most current version of the code see: https://github.com/jpadfield/simple-site

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    Software . 2021
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      Software . 2021
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    Authors: Haverals, Wouter; Joosen, Vanessa;

    This repository contains several items supplementing the article Constructing Age in Children’s Literature: A Digital Approach to Guus Kuijer’s Oeuvre [The Lion and the Unicorn, forthcoming] stylometry_kuijer.ipynb -- a Jupyter Notebook, containing the code to (re)run the stylometric analyses. Given that the original texts are copyrighted, they are not part of this repository. meta.xlsx -- a spreadsheet containing meta-information about the works of fiction authored by Guus Kuijer. scatterplot_kuijer.html -- an interactive scatterplot, comparing children and adolescent speech on the one hand, and adult and old adult speech on the other (made with the scattertext tool, developed by Jason Kessler).

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    Software . 2021
    License: CC BY
    Data sources: Datacite
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    Software . 2021
    License: CC BY
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      Software . 2021
      License: CC BY
      Data sources: Datacite
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      Software . 2021
      License: CC BY
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    gCube Catalogue (gCat) API is a library containing classes shared across gcat* components. gCube is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the D4Science Infrastructure, by favouring the realisation of reuse-oriented policies. gCube has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage. gCube offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data. D4Science is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube. The source code of this software version is available at: https://code-repo.d4science.org/gCubeSystem/gcat-api/releases/tag/v2.3.0

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    gCube Catalogue (gCat) Service allows any client to publish on the gCube Catalogue. gCube is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the D4Science Infrastructure, by favouring the realisation of reuse-oriented policies. gCube has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage. gCube offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data. D4Science is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube. The source code of this software version is available at: https://code-repo.d4science.org/gCubeSystem/gcat/releases/tag/v2.1.0

    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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    Authors: Sinibaldi, Fabio;

    gCube SDI is the set of engines and logic responsible of dealing with GIS data management in a gCube Infrastructure. In the image above is presented the SDI from a logic point of view : Orange components are all gCube SDI logic meant to facilitate the management of the SDI nodes and content (see #gCube Logic below), in particular : SDI-Service manages instances credentials on IS and some configuration operation on the nodes GeoServer and GeoNetwork are equipped with connectors in order to manage http(s) requests Thredds node are provisioned with a Data_Transfer_2 equipped with a dedicated How_to_use_Data_Transfer_2#Thredds_Plugin_Suite. Third party engines are exploited for their core GIS features (i.e. store/access to GIS data/metadata) The generic rationale of gCube logic is to provide : Context-oriented credential management, in order to enforce access policies to published (meta) Metadata enrichment in publication phase GIS (meta)data publication utilities NB : It is important to note that while the use of gCube logic is recommended, various use cases may directly exploit provided third party engines for various reasons (e.g. non-Java algorithms) Third Party Engines In gCube SDI, third party engines are exploited for their GIS data/metadata management, more in details we use : GeoNetwork : Store GIS ISO Metadata (xml) Expose metadata with CSW Harvest metadata GeoServer : Store GIS DATA (e.g. shp, postgis, geopackage) Expose data with WMS, WFS, WCS.. Thredds : Store GIS DATA Expose data with WMS, WFS, WCS.. Managed Credentials GeoNetwork credentials are managed by gCube org.gcube.spatial.data.geonetwork library and org.gcube.spatial.data.sdi-service SmartGear service. These credentials are generated as needed, and configured in such a way that metadata visibility between gCube contexts reflects gCube policies (more information here). GeoServer and Thredds credentials are loosely managed, meaning that only administrator user is used in order to publish data to these engines. gCube Logic During SDI evolution, distributed gCube logic evolved according to emerging needs while trying to maintain retro-compatibility. For this reason, some components may still be used while being deprecated (e.g. ws-thredds) and there is still some overlap between logic. Following list aims to provide a generic overview of provided gCube logic features by component : org.gcube.spatial.data.geonetwork Library Client for GeoNetwork service Metadata publication utilities Metadata enhancement (NB uses IS Generic Resource, more information at GeoNetwork_library#Metadata_generation_facilities) GeoNetwork credentials management (generation and retrieval) org.gcube.spatial.data.gis-interface Library Data publication utilities with contextual metadata publishing (uses org.gcube.spatial.data.geonetwork for metadata) Currently supported data engine is only GeoServer org.gcube.spatial.data.sdi-service SmartGear Service Credentials management and retrieval Metadata enhancement via template application (used in Thredds publication, see ws-thredds below) SDI configuration management Thredds Plugin Suite Data Transfer Plugins Configure catalogs in local Thredds Publish transferred dataset's metadata in VRE's GeoNewtork org.gcube.spatial.data.ws-thredds Deprecated Library Synchronize a ws-folder with a Thredds catalog, generating and publishing metadata on GeoNetwork Connectors These components are library which implement a Web Application Filter in order to : Intercept incoming http(s) requests If gcube-token is declared, then retrieve credentials from SDI Service and set them in the current request This allows for authentication within third party engines unaware of gCube logic, by using gcube-token. NB : this approach is considered obsolete and should be changed in favor of oauth integration. Available connectors are : GeoNetwork : org.gcube.data.access.geonetwork.gcube-geonetwork-connector GeoServer : org.gcube.data.access.geoserver.gcube-geoserver-connector

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    Authors: Nan, Bai; Renqian, Luo;

    WHOSe Heritage: Classification of UNESCO World Heritage "Outstanding Universal Value" Documents with Smoothed Labels This repository provides the supplemental materials for reproducing the results of the above-mentioned paper as submitted to arXiv preprint server, including both models and results.

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    Authors: Fabio Sinibaldi;

    The org.gcube.data.publishing.ckan2Zenodo gCube component is a Java library which translates CKAN items into Zenodo depositions, allowing to further editing and publication. The library is invoked by the client (in this case the gCube CKAN GUI), which relies on the gCat service for interacting with CKAN. After the ckan item is loaded, a default translation is then applied on the item's core fields generating in a Draft Zenodo Deposition. NB If the item has already a linked Zenodo DOI, the Draft Deposition overrides its specified informations. A XML Mapping associated with item's profile, is then loaded from the IS (token must be specified by the client). The XML Mapping extracts data from the CKAN item and applies them to the Draft Deposition, resulting in a Final Deposition. The Final Deposition is then returned to the client for further editing, which can eventually ask for its publication (the new Zenodo Doi will be then applied to the CKAN item through gCat).

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    Authors: Matzig, David N.;

    Description This package is a helpful wrapper around functions from mainly the Momocs (Bonhomme et al. 2014), EBImage (Pau et al. 2010), and imager (Barthelme et al. 2020) packages. It is designed for the fast and easy extraction of single outline shapes of, for example, stone tools from images containing multiple thereof, such as the ones present in archaeological publications. This release is provided with a testing dataset, using the Morar Quartz Industry image (Credit: Wellcome Collection, https://wellcomecollection.org/works/th7egtfj, distributed under CC BY 4.0). A brief explanation of the workflow and the package functions can be found on github.com/yesdavid/outlineR. References Barthelme et al. 2020: Barthelme, S., Tschumperle, D., Wijffels, J., Assemlal, H. E., & Ochi, S. (2020). imager: Image Processing Library Based on “CImg” (0.42.3) [Computer software]. https://CRAN.R-project.org/package=imager Bonhomme et al. 2014: Bonhomme, V., Picq, S., Gaucherel, C., & Claude, J. (2014). Momocs: Outline Analysis Using R. Journal of Statistical Software, 56(13). https://doi.org/10.18637/jss.v056.i13 Pau et al. 2010: Pau, G., Fuchs, F., Sklyar, O., Boutros, M., & Huber, W. (2010). EBImage—An R package for image processing with applications to cellular phenotypes. Bioinformatics, 26(7), 979–981. https://doi.org/10.1093/bioinformatics/btq046

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    Authors: Joseph Padfield;

    This is a simple set of processes for creating a standard set of webpages based on a simple set of json files. This project is intended to work along side other projects to provide a simple way of creating a set of consistent webpages, which can be delivered as part of your own GitHub project using GitHub pages. It has been extended to allow more complex features such as presenting IIIIF (https://iiif.io) viewers, Timelines, and ordered Lists & Galleries.

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  • Authors: Joseph Padfield;

    This is an interactive live modelling system which can automatically convert simple tab separated triples or JSON-LD into graphical models using the mermaid library. General updates and improvements have been carried out, with the addition of the Mermaid SubGraph functionality to aid the organisation of more complex models. Instructions: Full details and instructions relating to how this system works is still being developed, however several examples are included in the interactive web site: dynamic modelling, with all of the related code presented in GitHub.

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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: Joseph Padfield;

    This is a simple set of processes for creating a standard set of webpages based on a simple set of json files. This project is intended to work along side other projects to provide a simple way of creating a set of consistent webpages, which can be delivered as part of your own GitHub project using GitHub pages. It has been extended to allow more complex features such as presenting IIIIF (https://iiif.io) viewers, Timelines, and ordered Lists & Galleries. Various updates to the related JavaScript libraries have been added along with an option to use the whole system to create dynamic as well as static websites. For more detail and the most current version of the code see: https://github.com/jpadfield/simple-site

    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
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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: Haverals, Wouter; Joosen, Vanessa;

    This repository contains several items supplementing the article Constructing Age in Children’s Literature: A Digital Approach to Guus Kuijer’s Oeuvre [The Lion and the Unicorn, forthcoming] stylometry_kuijer.ipynb -- a Jupyter Notebook, containing the code to (re)run the stylometric analyses. Given that the original texts are copyrighted, they are not part of this repository. meta.xlsx -- a spreadsheet containing meta-information about the works of fiction authored by Guus Kuijer. scatterplot_kuijer.html -- an interactive scatterplot, comparing children and adolescent speech on the one hand, and adult and old adult speech on the other (made with the scattertext tool, developed by Jason Kessler).

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    ZENODO
    Software . 2021
    License: CC BY
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    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/

    gCube Catalogue (gCat) API is a library containing classes shared across gcat* components. gCube is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the D4Science Infrastructure, by favouring the realisation of reuse-oriented policies. gCube has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage. gCube offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data. D4Science is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube. The source code of this software version is available at: https://code-repo.d4science.org/gCubeSystem/gcat-api/releases/tag/v2.3.0

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    gCube Catalogue (gCat) Service allows any client to publish on the gCube Catalogue. gCube is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the D4Science Infrastructure, by favouring the realisation of reuse-oriented policies. gCube has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage. gCube offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data. D4Science is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube. The source code of this software version is available at: https://code-repo.d4science.org/gCubeSystem/gcat/releases/tag/v2.1.0

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      Data sources: Datacite
      ZENODO
      Software . 2022
      Data sources: ZENODO
      ZENODO
      Software . 2022
      Data sources: ZENODO
      ZENODO
      Software . 2022
      Data sources: ZENODO
      ZENODO
      Software . 2021
      Data sources: ZENODO
      ZENODO
      Software . 2022
      Data sources: ZENODO
      ZENODO
      Software . 2022
      Data sources: ZENODO
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    Authors: Sinibaldi, Fabio;

    gCube SDI is the set of engines and logic responsible of dealing with GIS data management in a gCube Infrastructure. In the image above is presented the SDI from a logic point of view : Orange components are all gCube SDI logic meant to facilitate the management of the SDI nodes and content (see #gCube Logic below), in particular : SDI-Service manages instances credentials on IS and some configuration operation on the nodes GeoServer and GeoNetwork are equipped with connectors in order to manage http(s) requests Thredds node are provisioned with a Data_Transfer_2 equipped with a dedicated How_to_use_Data_Transfer_2#Thredds_Plugin_Suite. Third party engines are exploited for their core GIS features (i.e. store/access to GIS data/metadata) The generic rationale of gCube logic is to provide : Context-oriented credential management, in order to enforce access policies to published (meta) Metadata enrichment in publication phase GIS (meta)data publication utilities NB : It is important to note that while the use of gCube logic is recommended, various use cases may directly exploit provided third party engines for various reasons (e.g. non-Java algorithms) Third Party Engines In gCube SDI, third party engines are exploited for their GIS data/metadata management, more in details we use : GeoNetwork : Store GIS ISO Metadata (xml) Expose metadata with CSW Harvest metadata GeoServer : Store GIS DATA (e.g. shp, postgis, geopackage) Expose data with WMS, WFS, WCS.. Thredds : Store GIS DATA Expose data with WMS, WFS, WCS.. Managed Credentials GeoNetwork credentials are managed by gCube org.gcube.spatial.data.geonetwork library and org.gcube.spatial.data.sdi-service SmartGear service. These credentials are generated as needed, and configured in such a way that metadata visibility between gCube contexts reflects gCube policies (more information here). GeoServer and Thredds credentials are loosely managed, meaning that only administrator user is used in order to publish data to these engines. gCube Logic During SDI evolution, distributed gCube logic evolved according to emerging needs while trying to maintain retro-compatibility. For this reason, some components may still be used while being deprecated (e.g. ws-thredds) and there is still some overlap between logic. Following list aims to provide a generic overview of provided gCube logic features by component : org.gcube.spatial.data.geonetwork Library Client for GeoNetwork service Metadata publication utilities Metadata enhancement (NB uses IS Generic Resource, more information at GeoNetwork_library#Metadata_generation_facilities) GeoNetwork credentials management (generation and retrieval) org.gcube.spatial.data.gis-interface Library Data publication utilities with contextual metadata publishing (uses org.gcube.spatial.data.geonetwork for metadata) Currently supported data engine is only GeoServer org.gcube.spatial.data.sdi-service SmartGear Service Credentials management and retrieval Metadata enhancement via template application (used in Thredds publication, see ws-thredds below) SDI configuration management Thredds Plugin Suite Data Transfer Plugins Configure catalogs in local Thredds Publish transferred dataset's metadata in VRE's GeoNewtork org.gcube.spatial.data.ws-thredds Deprecated Library Synchronize a ws-folder with a Thredds catalog, generating and publishing metadata on GeoNetwork Connectors These components are library which implement a Web Application Filter in order to : Intercept incoming http(s) requests If gcube-token is declared, then retrieve credentials from SDI Service and set them in the current request This allows for authentication within third party engines unaware of gCube logic, by using gcube-token. NB : this approach is considered obsolete and should be changed in favor of oauth integration. Available connectors are : GeoNetwork : org.gcube.data.access.geonetwork.gcube-geonetwork-connector GeoServer : org.gcube.data.access.geoserver.gcube-geoserver-connector

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    ZENODO
    Software . 2021
    Data sources: Datacite
    ZENODO
    Software . 2021
    Data sources: ZENODO
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      ZENODO
      Software . 2021
      Data sources: Datacite
      ZENODO
      Software . 2021
      Data sources: ZENODO
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    Authors: Nan, Bai; Renqian, Luo;

    WHOSe Heritage: Classification of UNESCO World Heritage "Outstanding Universal Value" Documents with Smoothed Labels This repository provides the supplemental materials for reproducing the results of the above-mentioned paper as submitted to arXiv preprint server, including both models and results.

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    Authors: Fabio Sinibaldi;

    The org.gcube.data.publishing.ckan2Zenodo gCube component is a Java library which translates CKAN items into Zenodo depositions, allowing to further editing and publication. The library is invoked by the client (in this case the gCube CKAN GUI), which relies on the gCat service for interacting with CKAN. After the ckan item is loaded, a default translation is then applied on the item's core fields generating in a Draft Zenodo Deposition. NB If the item has already a linked Zenodo DOI, the Draft Deposition overrides its specified informations. A XML Mapping associated with item's profile, is then loaded from the IS (token must be specified by the client). The XML Mapping extracts data from the CKAN item and applies them to the Draft Deposition, resulting in a Final Deposition. The Final Deposition is then returned to the client for further editing, which can eventually ask for its publication (the new Zenodo Doi will be then applied to the CKAN item through gCat).

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    ZENODO
    Software . 2021
    Data sources: Datacite
    ZENODO
    Software . 2021
    Data sources: ZENODO
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      ZENODO
      Software . 2021
      Data sources: Datacite
      ZENODO
      Software . 2021
      Data sources: ZENODO
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    Authors: Matzig, David N.;

    Description This package is a helpful wrapper around functions from mainly the Momocs (Bonhomme et al. 2014), EBImage (Pau et al. 2010), and imager (Barthelme et al. 2020) packages. It is designed for the fast and easy extraction of single outline shapes of, for example, stone tools from images containing multiple thereof, such as the ones present in archaeological publications. This release is provided with a testing dataset, using the Morar Quartz Industry image (Credit: Wellcome Collection, https://wellcomecollection.org/works/th7egtfj, distributed under CC BY 4.0). A brief explanation of the workflow and the package functions can be found on github.com/yesdavid/outlineR. References Barthelme et al. 2020: Barthelme, S., Tschumperle, D., Wijffels, J., Assemlal, H. E., & Ochi, S. (2020). imager: Image Processing Library Based on “CImg” (0.42.3) [Computer software]. https://CRAN.R-project.org/package=imager Bonhomme et al. 2014: Bonhomme, V., Picq, S., Gaucherel, C., & Claude, J. (2014). Momocs: Outline Analysis Using R. Journal of Statistical Software, 56(13). https://doi.org/10.18637/jss.v056.i13 Pau et al. 2010: Pau, G., Fuchs, F., Sklyar, O., Boutros, M., & Huber, W. (2010). EBImage—An R package for image processing with applications to cellular phenotypes. Bioinformatics, 26(7), 979–981. https://doi.org/10.1093/bioinformatics/btq046

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    ZENODO
    Software . 2021
    Data sources: Datacite
    ZENODO
    Software . 2021
    Data sources: ZENODO
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      ZENODO
      Software . 2021
      Data sources: Datacite
      ZENODO
      Software . 2021
      Data sources: ZENODO
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    Authors: Joseph Padfield;

    This is a simple set of processes for creating a standard set of webpages based on a simple set of json files. This project is intended to work along side other projects to provide a simple way of creating a set of consistent webpages, which can be delivered as part of your own GitHub project using GitHub pages. It has been extended to allow more complex features such as presenting IIIIF (https://iiif.io) viewers, Timelines, and ordered Lists & Galleries.

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