Make research reproducible again
Stian Soiland-Reyes, Norman Morrison, Carole Goble
eScience lab, University of Manchester
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.
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
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
Research
Objects
in the wild
Apache Taverna: Data Bundle
Data Bundle API
SCUFL2 Workflow Bundle
Manifest
Annotation
Annotation
Annotation
Workflow
Workflow
Workflow
Profile
Profile
Tool Config
Tool Config
Tool Config
Tool 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
Smart Containers
Citation and attribution
Include all relevant sources
Exchange mechanism
Extensible metadata
Enabling reproducibility
.. but how do we prove it?
Benefits of Research Objects
Norman Morrison