Make research reproducible 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

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

2016-05-18 Make research reproducible again - researchobject.org

By Stian Soiland-Reyes

2016-05-18 Make research reproducible again - researchobject.org

CWL Hackathon, Paris

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