2016-05-18-make research reproducible again - researchobject.org
TRANSCRIPT
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Make researchMake researchreproducible 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, 2016-05-18This work is licensed under a
.Creative Commons Attribution 4.0 International License
researchobject.org
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What is in a Research Object?What is in a Research Object?
A Research Object bundles and relates digitalresources of a scientific experiment orinvestigation:
Data used and results produced in experimentalstudyMethods employed to produce and analyse thatdataProvenance and settings for the experimentsPeople involved in the investigationAnnotations about these resources, to improveunderstanding and interpretation
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id: doi:10.15490/seek.1.investigation.56createdOn: 2015-07-10T16:46:00ZcreatedBy: 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
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https://github.com/ResearchObject/ro-tutorials
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ResearchResearchObjectsObjects
in the wildin the wild
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http://taverna.incubator.apache.org/
Apache Taverna: Data BundleApache Taverna: Data Bundle
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https://taverna.incubator.apache.org/download/language/
Data Bundle APIData Bundle API
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SCUFL2 Workflow BundleSCUFL2 Workflow Bundle
Manifest AnnotationAnnotationAnnotation
WorkflowWorkflowWorkflow
ProfileProfile
Tool ConfigTool ConfigTool ConfigTool Config
main workflow
main profile
Provenance
Docker image
CWL tool desc
ExampleRun
CWL tool descReference
Data Docker imageapplication/vnd.taverna.scufl2.workflow-bundle
https://taverna.incubator.apache.org/documentation/scufl2/
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https://daspos.crc.nd.edu/
Smart Containers
http://ceur-ws.org/Vol-1486/paper_89.pdf
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doi:10.1111/febs.13237
doi:10.15490/seek.1.investigation.56
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Citation and attributionInclude all relevant sources
Exchange mechanismExtensible metadata
Enabling reproducibility.. but how do we prove it?
Benefits ofBenefits ofResearch ObjectsResearch Objects
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Norman Morrison http://researchobject.org/http://fair-dom.org/http://www.seek4science.org/http://www.farrinstitute.org/http://www.wf4ever-project.orghttp://myexperiment.org/