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

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://w3id.org/ro/

https://w3id.org/bundle/

https://github.com/ResearchObject/bagit-ro

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

https://www.fairdomhub.org/investigations/58

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

doi:10.1371/journal.pone.0127612

https://isa-tools.github.io/soapdenovo2/

Norman Morrison http://researchobject.org/http://fair-dom.org/http://www.seek4science.org/http://www.farrinstitute.org/http://www.wf4ever-project.orghttp://myexperiment.org/