Project deliverable Open Access

BioExcel Deliverable D2.4 - Final Release of Workflows and Modular Tools for User Services

Hospital, Adam; Montras, Anna; Gelpí, Josep Lluís; Lezzi, Daniele; Badia, Rosa Maria; Newhouse, Steven; Dianes, Jose Antonio; Andrio, Pau; Jordà, Luís; Soiland-Reyes, Stian; White, Darren J; Carter, Adam; Ippoliti, Emiliano; Melquiond, Adrien; de Groot, Bert


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{
  "description": "<p>This deliverable presents the final release of workflows and modular tools designed and developed in the BioExcel project during the last three years. A summary of the software development process adopted, following a set of best practices promoted by ELIXIR, is exposed together with examples of working implementations. Availability of the building blocks and workflows produced so far by the project is listed, describing where to find them and how can they be installed and used, presenting a variety of approaches designed for different types of users.</p>\n\n<p>The current stage of the Model Protein Mutants transversal workflow, used as a pivot study and demonstrator for the workflows software library development, is revised. Also, two scientific success stories achieved using this pipeline are presented, showing the potential of the methodology in a real scenario. The current implementation for each of the project pilot use cases is detailed, with special focus on the workflows behind them, availability and feedback.</p>\n\n<p>Finally, the services provided and the present phase for the two deployment environments, development and production, is outlined. An overview of the tools developed and those currently available in each of the cloud and HPC infrastructures is given. Particularly successful use cases produced by the BSC testbed and the BioExcel Cloud Portal are depicted.</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Institute for Research in Biomedicine (IRB-Barcelona)", 
      "@type": "Person", 
      "name": "Hospital, Adam"
    }, 
    {
      "affiliation": "Institute for Research in Biomedicine (IRB-Barcelona)", 
      "@type": "Person", 
      "name": "Montras, Anna"
    }, 
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@type": "Person", 
      "name": "Gelp\u00ed, Josep Llu\u00eds"
    }, 
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@type": "Person", 
      "name": "Lezzi, Daniele"
    }, 
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@type": "Person", 
      "name": "Badia, Rosa Maria"
    }, 
    {
      "affiliation": "European Bioinformatics Institute, EMBL-EBI", 
      "@type": "Person", 
      "name": "Newhouse, Steven"
    }, 
    {
      "affiliation": "European Bioinformatics Institute, EMBL-EBI", 
      "@type": "Person", 
      "name": "Dianes, Jose Antonio"
    }, 
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@type": "Person", 
      "name": "Andrio, Pau"
    }, 
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@type": "Person", 
      "name": "Jord\u00e0, Lu\u00eds"
    }, 
    {
      "affiliation": "University of Manchester", 
      "@type": "Person", 
      "name": "Soiland-Reyes, Stian"
    }, 
    {
      "affiliation": "Edinburgh Parallel Computing Centre, EPCC", 
      "@type": "Person", 
      "name": "White, Darren J"
    }, 
    {
      "affiliation": "Edinburgh Parallel Computing Centre, EPCC", 
      "@type": "Person", 
      "name": "Carter, Adam"
    }, 
    {
      "affiliation": "Forschungszentrum J\u00fclich - J\u00fclich Supercomputing Centre (JSC)", 
      "@type": "Person", 
      "name": "Ippoliti, Emiliano"
    }, 
    {
      "affiliation": "University of Utrecht", 
      "@type": "Person", 
      "name": "Melquiond, Adrien"
    }, 
    {
      "affiliation": "Max Planck Institute for Biophysical Chemistry, G\u00f6ttingen", 
      "@type": "Person", 
      "name": "de Groot, Bert"
    }
  ], 
  "url": "https://zenodo.org/record/3236256", 
  "datePublished": "2019-05-31", 
  "version": "1", 
  "keywords": [
    "Workflows", 
    "HPC", 
    "Biomolecular simulations"
  ], 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.3236256", 
  "@id": "https://doi.org/10.5281/zenodo.3236256", 
  "@type": "CreativeWork", 
  "name": "BioExcel Deliverable D2.4 - Final Release of Workflows and Modular Tools for User Services"
}
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