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Using a suite of ontologies for preserving workflow-centric research objects
9 references·16 citing·37 second hop
Using a suite of ontologies for preserving workflow-centric research objects (2015)Using a suite of ontologies for preservin…An introduction to Docker for reproducible research (2015)An introduction to Docker for…Best Practices for Scientific Computing (2014)Best Practices for Scientific…Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research (2014)Best Practices for Computatio…The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)The Taverna workflow suite: d…Wings: Intelligent Workflow-Based Design of Computational Experiments (2010)Wings: Intelligent Workflow-B…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Galaxy: a comprehensive appro…Workflows and e-Science: An overview of workflow system features and capabilities (2008)Workflows and e-Science: An o…The design and realisation of the Virtual Research Environment for social sharing of workflows (2008)The design and realisation of…VisTrails (2006)VisTrailsRecording provenance of workflow runs with RO-Crate (2024)Recording provenance of workf…Design considerations for workflow management systems use in production genomics research and the clinic (2021)Design considerations for wor…Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv (2019)Sharing interoperable workflo…Modeling Digital Humanities Collections as Research Objects (2019)Modeling Digital Humanities C…Utilizing Provenance in Reusable Research Objects (2018)Utilizing Provenance in Reusa…Enabling precision medicine via standard communication of HTS provenance, analysis, and results (2018)Enabling precision medicine v…Why good data analysts need to be critical synthesists. Determining the role of semantics in data analysis (2017)Why good data analysts need t…Using Ontologies for Verification and Validation of Workflow-Based Experiments (2017)Using Ontologies for Verifica…Sciunits: Reusable Research Objects (2017)Sciunits: Reusable Research O…Scientific workflows: Past, present and future (2017)Scientific workflows: Past, p…Abstract, link, publish, exploit: An end to end framework for workflow sharing (2017)Abstract, link, publish, expl…A Templating System to Generate Provenance (2017)A Templating System to Genera…Scientific Workflows (2016)Scientific WorkflowsRABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS (2016)RABIX: AN OPEN-SOURCE WORKFLO…A framework for scientific workflow reproducibility in the cloud (2016)A framework for scientific wo…From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics (2015)From Peer-Reviewed to Peer-Re…Reproducible Research in Computational Science (2011)Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation (2016)Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)Automated assessment of psychiatric disorders using speech: A systematic review (2020)Taverna: a tool for building and running workflows of services (2006)AiiDA: automated interactive infrastructure and database for computational science (2015)A review of bioinformatic pipeline frameworks (2016)BioContainers: an open-source and community-driven framework for software standardization (2017)Design Patterns: Elements of Reusable Object-Oriented Software (1994)Bioconductor: open software development for computational biology and bioinformatics (2004)Snakemake—a scalable bioinformatics workflow engine (2012)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Nextflow enables reproducible computational workflows (2017)Taverna: lessons in creating a workflow environment for the life sciences (2005)Workflows For E-Science: Scientific Workflows For Grids (2007)myExperiment: a repository and social network for the sharing of bioinformatics workflows (2010)4 What Is Web 2.0? 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(2017)Our path to better science in less time using open data science tools (2017)A Large-Scale Study About Quality and Reproducibility of Jupyter Notebooks (2019)Provenance and scientific workflows (2008)SPADE: Support for Provenance Auditing in Distributed Environments (2012)A survey on provenance: What for? What form? What from? (2017)
this work references cited by second hop

References

  • 2010Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences3,455 cited
  • 2015An introduction to Docker for reproducible research1,058 cited
  • 2008Workflows and e-Science: An overview of workflow system features and capabilities832 cited
  • 2014Best Practices for Scientific Computing715 cited
  • 2013The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud678 cited
  • 2006VisTrails480 cited
  • 2008The design and realisation of the Virtual Research Environment for social sharing of workflows432 cited
  • 2010Wings: Intelligent Workflow-Based Design of Computational Experiments201 cited
  • 2014Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research140 cited

Cited by

  • 2017Scientific workflows: Past, present and future131 cited
  • 2016Scientific Workflows106 cited
  • 2019Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv81 cited
  • 2017Sciunits: Reusable Research Objects54 cited
  • 2017A Templating System to Generate Provenance52 cited

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2024
Recording provenance of workflow runs with RO-Crate
47 cited
  • 2021Design considerations for workflow management systems use in production genomics research and the clinic43 cited
  • 2015From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics41 cited
  • 2017Why good data analysts need to be critical synthesists. Determining the role of semantics in data analysis40 cited
  • 2018Enabling precision medicine via standard communication of HTS provenance, analysis, and results37 cited
  • 2016RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS33 cited
  • 2016A framework for scientific workflow reproducibility in the cloud29 cited
  • 2017Abstract, link, publish, exploit: An end to end framework for workflow sharing29 cited
  • 2017Using Ontologies for Verification and Validation of Workflow-Based Experiments27 cited
  • 2019Modeling Digital Humanities Collections as Research Objects27 cited
  • 2018Utilizing Provenance in Reusable Research Objects24 cited