Presented at: 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

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. researchobject.org

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

6. 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

8. https://w3id.org/ro/

9. https://w3id.org/bundle/

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

11. https://github.com/ResearchObject/ro-tutorials

12. ResearchResearch
ObjectsObjects
in the wildin the wild

13. http://taverna.incubator.apache.org/
Apache Taverna: Data BundleApache Taverna: Data Bundle

14. https://taverna.incubator.apache.org/download/language/
Data Bundle APIData Bundle API

15. 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/

16. https://daspos.crc.nd.edu/
Smart Containers
http://ceur-ws.org/Vol-1486/paper_89.pdf

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

19. doi:10.1111/febs.13237
doi:10.15490/seek.1.investigation.56

20. 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

21. doi:10.1371/journal.pone.0127612

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

24. 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/