Introduction: What do we mean by citable data and reproducible models?
Carole Goble, Wolfgang Müller, Dagmar WaltemathFAIRDOM ConsortiumThe University of Manchester, [email protected]
EraSysAPP Workshop Data Citation and Model Reproducibility, Rostock, 14-16 Sept 2015
“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
Reproducible Codes and Available Data
Why Unreproducible Research Happens
• Tainted resources• Black boxes• Poor Reporting• Unavailable
resources / results: data, software • Bad maths
• Sins of omission• Poor training,
sloppinesshttps://www.sciencenews.org/article/12-reasons-research-goes-wrong (adapted)
Ioannidis, Why Most Published Research Findings Are False, August 2005Joppa, et al, Troubling Trends in Scientific Software Use 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
FAIR ReproducibilityFind, Access, Interoperate, Reuse
FAIR Publishing
Catalogues Data specific Public Archives
Commons & Cross Resource Infra Portable Packaging
STANDARDS
Standards
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
Citable Data
• Persistent Identifiers• Resolution• Citation attribution• Credit lists• Citation infrastructure• Snapshots and versioning• Link Data with Publications
submit articleand 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
submit articleand move on…
publish article
Research Environment
Publication Environment
Peer Review
Citing data in research articles: principles, implementation, challenges – and the benefits of changing our waysJohanna 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
submit articleand move on…
publish article
Research Environment
Publication Environment
Peer Review
Standards for reproducibility of model-based resultsDagmar 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
submit articleand move on…
publish article
Research Environment
Publication Environment
Peer Review
Hands On