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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  <identifier identifierType="DOI">10.5281/zenodo.3236256</identifier>
  <creators>
    <creator>
      <creatorName>Hospital, Adam</creatorName>
      <givenName>Adam</givenName>
      <familyName>Hospital</familyName>
      <affiliation>Institute for Research in Biomedicine (IRB-Barcelona)</affiliation>
    </creator>
    <creator>
      <creatorName>Montras, Anna</creatorName>
      <givenName>Anna</givenName>
      <familyName>Montras</familyName>
      <affiliation>Institute for Research in Biomedicine (IRB-Barcelona)</affiliation>
    </creator>
    <creator>
      <creatorName>Gelpí, Josep Lluís</creatorName>
      <givenName>Josep Lluís</givenName>
      <familyName>Gelpí</familyName>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
    <creator>
      <creatorName>Lezzi, Daniele</creatorName>
      <givenName>Daniele</givenName>
      <familyName>Lezzi</familyName>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
    <creator>
      <creatorName>Badia, Rosa Maria</creatorName>
      <givenName>Rosa Maria</givenName>
      <familyName>Badia</familyName>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
    <creator>
      <creatorName>Newhouse, Steven</creatorName>
      <givenName>Steven</givenName>
      <familyName>Newhouse</familyName>
      <affiliation>European Bioinformatics Institute, EMBL-EBI</affiliation>
    </creator>
    <creator>
      <creatorName>Dianes, Jose Antonio</creatorName>
      <givenName>Jose Antonio</givenName>
      <familyName>Dianes</familyName>
      <affiliation>European Bioinformatics Institute, EMBL-EBI</affiliation>
    </creator>
    <creator>
      <creatorName>Andrio, Pau</creatorName>
      <givenName>Pau</givenName>
      <familyName>Andrio</familyName>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
    <creator>
      <creatorName>Jordà, Luís</creatorName>
      <givenName>Luís</givenName>
      <familyName>Jordà</familyName>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
    <creator>
      <creatorName>Soiland-Reyes, Stian</creatorName>
      <givenName>Stian</givenName>
      <familyName>Soiland-Reyes</familyName>
      <affiliation>University of Manchester</affiliation>
    </creator>
    <creator>
      <creatorName>White, Darren J</creatorName>
      <givenName>Darren J</givenName>
      <familyName>White</familyName>
      <affiliation>Edinburgh Parallel Computing Centre, EPCC</affiliation>
    </creator>
    <creator>
      <creatorName>Carter, Adam</creatorName>
      <givenName>Adam</givenName>
      <familyName>Carter</familyName>
      <affiliation>Edinburgh Parallel Computing Centre, EPCC</affiliation>
    </creator>
    <creator>
      <creatorName>Ippoliti, Emiliano</creatorName>
      <givenName>Emiliano</givenName>
      <familyName>Ippoliti</familyName>
      <affiliation>Forschungszentrum Jülich - Jülich Supercomputing Centre (JSC)</affiliation>
    </creator>
    <creator>
      <creatorName>Melquiond, Adrien</creatorName>
      <givenName>Adrien</givenName>
      <familyName>Melquiond</familyName>
      <affiliation>University of Utrecht</affiliation>
    </creator>
    <creator>
      <creatorName>de Groot, Bert</creatorName>
      <givenName>Bert</givenName>
      <familyName>de Groot</familyName>
      <affiliation>Max Planck Institute for Biophysical Chemistry, Göttingen</affiliation>
    </creator>
  </creators>
  <titles>
    <title>BioExcel Deliverable D2.4 - Final Release of Workflows and Modular Tools for User Services</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>Workflows</subject>
    <subject>HPC</subject>
    <subject>Biomolecular simulations</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-05-31</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Project deliverable</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3236256</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3236255</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/bioexcel</relatedIdentifier>
  </relatedIdentifiers>
  <version>1</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/675728/">675728</awardNumber>
      <awardTitle>Centre of Excellence for Biomolecular Research</awardTitle>
    </fundingReference>
  </fundingReferences>
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