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2016-05-18-Make research reproducible again - researchobject.org

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Bioinformatics Technical Hackathon: Tools, Workflows and Workbenches
Institut Pasteur, Paris, 2016-05-18

Source: http://slides.com/soilandreyes/2016-05-18-make-research-reproducible-again

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2016-05-18-Make research reproducible again - researchobject.org

  1. 1. Make researchMake research reproducible againreproducible again Stian Soiland-Reyes, Norman Morrison, Carole Goble eScience lab, University of Manchester @soilandreyes http://orcid.org/0000-0001-9842-9718 http://slides.com/soilandreyes/ Bioinformatics Technical Hackathon: Tools, Workflows and Workbenches Institut Pasteur, Paris, 2016-05-18 This work is licensed under a .Creative Commons Attribution 4.0 International License researchobject.org
  2. 2. researchobject.org
  3. 3. What is in a Research Object?What is in a Research Object? A Research Object bundles and relates digital resources of a scientific experiment or investigation: Data used and results produced in experimental study Methods employed to produce and analyse that data Provenance and settings for the experiments People involved in the investigation Annotations about these resources, to improve understanding and interpretation
  4. 4. id: doi:10.15490/seek.1.investigation.56 createdOn: 2015-07-10T16:46:00Z createdBy: http://orcid.org/0000-0001-9842-9718 aggregates: - id: /sequence/specimen5.bam conformsTo: http://gemrb.org/iesdp/file_formats/ie_formats/bam_v1.htm - id: http://example.com/blog/about-specimen5 authoredBy: http://orcid.org/0000-0001-7066-3350 - id: http://www.myexperiment.org/workflows/3355 history: provenance/workflow-evolution.ttl annotations: - about: /sequence/specimen5.bam content: annotations/specimen5-properties.jsonld createdBy: http://orcid.org/0000-0001-7066-3350 - about: /sequence/specimen5.bam content: http://example.com/blog/about-specimen5 motivatedBy: oa:questioning
  5. 5. https://w3id.org/ro/
  6. 6. https://w3id.org/bundle/
  7. 7. https://github.com/ResearchObject/bagit-ro
  8. 8. https://github.com/ResearchObject/ro-tutorials
  9. 9. ResearchResearch ObjectsObjects in the wildin the wild
  10. 10. http://taverna.incubator.apache.org/ Apache Taverna: Data BundleApache Taverna: Data Bundle
  11. 11. https://taverna.incubator.apache.org/download/language/ Data Bundle APIData Bundle API
  12. 12. SCUFL2 Workflow BundleSCUFL2 Workflow Bundle Manifest AnnotationAnnotation Annotation WorkflowWorkflow Workflow Profile Profile Tool ConfigTool Config Tool ConfigTool Config main workflow main profile Provenance Docker image CWL tool desc Example Run CWL tool desc Reference Data Docker image application/vnd.taverna.scufl2.workflow-bundle https://taverna.incubator.apache.org/documentation/scufl2/
  13. 13. https://daspos.crc.nd.edu/ Smart Containers http://ceur-ws.org/Vol-1486/paper_89.pdf
  14. 14. https://www.fairdomhub.org/investigations/58
  15. 15. doi:10.1111/febs.13237 doi:10.15490/seek.1.investigation.56
  16. 16. Citation and attribution Include all relevant sources Exchange mechanism Extensible metadata Enabling reproducibility .. but how do we prove it? Benefits ofBenefits of Research ObjectsResearch Objects
  17. 17. doi:10.1371/journal.pone.0127612
  18. 18. https://isa-tools.github.io/soapdenovo2/
  19. 19. Norman Morrison http://researchobject.org/ http://fair-dom.org/ http://www.seek4science.org/ http://www.farrinstitute.org/ http://www.wf4ever-project.org http://myexperiment.org/

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