Post on 12-Apr-2017
transcript
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
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
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
https://github.com/ResearchObject/ro-tutorials
ResearchResearchObjectsObjects
in the wildin the wild
http://taverna.incubator.apache.org/
Apache Taverna: Data BundleApache Taverna: Data Bundle
https://taverna.incubator.apache.org/download/language/
Data Bundle APIData Bundle API
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/
https://daspos.crc.nd.edu/
Smart Containers
http://ceur-ws.org/Vol-1486/paper_89.pdf
doi:10.1111/febs.13237
doi:10.15490/seek.1.investigation.56
Citation and attributionInclude all relevant sources
Exchange mechanismExtensible metadata
Enabling reproducibility.. but how do we prove it?
Benefits ofBenefits ofResearch ObjectsResearch Objects
Norman Morrison http://researchobject.org/http://fair-dom.org/http://www.seek4science.org/http://www.farrinstitute.org/http://www.wf4ever-project.orghttp://myexperiment.org/