1.
Introduction:
What do we mean by citable
data and reproducible
models?
Carole Goble, Wolfgang Müller, Dagmar Waltemath
FAIRDOM Consortium
The University of Manchester, UK
carole.goble@manchester.ac.uk
EraSysAPP Workshop Data Citation and Model Reproducibility, Rostock, 14-16 Sept 2015

2.
“An article about
computational science in a
scientific publication is not
the scholarship itself, it is
merely advertising of the
scholarship. The actual
scholarship is the complete
software development
environment, [the complete
data] and the complete set
of instructions which
generated the figures.”
David Donoho, “Wavelab and
Reproducible Research,” 1995

3.
Reproducible Codes and Available Data

4.
Why Unreproducible Research Happens
• Tainted resources
• Black boxes
• Poor Reporting
• Unavailable resources /
results: data, software
• Bad maths
• Sins of omission
• Poor training,
sloppiness
https://www.sciencenews.org/article/12-reasons-research-goes-wrong (adapted)
Ioannidis, Why Most Published Research Findings Are False, August 2005
Joppa, et al,TroublingTrends inScientificSoftwareUse SCIENCE 340 May 2013
Scientific method
• Impact factor mania
• Pressure to publish
• Broken peer review
• Research never reported
• Disorganisation
• Time pressures
• Prep & curate costs
Social environment

5.
FAIR Reproducibility
Find, Access, Interoperate, Reuse

6.
FAIR Publishing
Catalogues Data specific
Public Archives
Commons & Cross
Resource Infra Portable Packaging
STANDARDS

7.
Standards

8.
Packaging, Porting, Reusing
Bergman et al COMBINE archive and OMEX format: one file to
share all information to reproduce a modeling project, BMC
Bioinformatics 2014, 15:369

9.
Citable Data
• Persistent Identifiers
• Resolution
• Citation attribution
• Credit lists
• Citation infrastructure
• Snapshots and versioning
• Link Data with Publications

10.
submit article
and move on…
publish article
Research
Environment
Publication
Environment
Peer
Review
• Find, Access,
Interoperate, Reuse
– Catalogues, Public
Archives, Licensing,
Guidelines, Standards
– Packaging models and
Data
• Data / Software
Publishing
– Link Data / Software and
Literature
• Credit and citation

11.
submit article
and move on…
publish article
Research
Environment
Publication
Environment
Peer
Review
Citing data in research articles:
principles, implementation,
challenges – and the benefits of
changing our ways
Johanna McEntyre (Mon)
Publishing data and code
openly Tom Ingraham (Mon)
The FAIRDOM Commons for
Systems Biology Carole Goble
(Mon)
The OpenAIRE infrastructure and
RDA Data Publishing Working
Group: results and vision Paolo
Manghi (Wed)
Data

12.
submit article
and move on…
publish article
Research
Environment
Publication
Environment
Peer
Review
Standards for reproducibility of
model-based results
Dagmar Waltemath (Tues)
Reproducible model construction,
validation and simulation
Jacky Snoep (Tues)
Capturing the context – one
small(ish) step for modellers,
one giant leap for mankind
Mihai Glont (Tues)
Archiving modeling results
Finn Bacall, Stuart
Owen, Martin Scharm (Weds)
Models

13.
submit article
and move on…
publish article
Research
Environment
Publication
Environment
Peer
Review
Hands On