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Introduction: What do we mean by citable data and reproducible models? Carole Goble, Wolfgang Müller, Dagmar Waltemath FAI...
“An article about computational science in a scientific publication is not the scholarship itself, it is merely advertisin...
Reproducible Codes and Available Data
Why Unreproducible Research Happens • Tainted resources • Black boxes • Poor Reporting • Unavailable resources / results: ...
FAIR Reproducibility Find, 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 ...
Citable Data • Persistent Identifiers • Resolution • Citation attribution • Credit lists • Citation infrastructure • Snaps...
submit article and move on… publish article Research Environment Publication Environment Peer Review • Find, Access, Inter...
submit article and move on… publish article Research Environment Publication Environment Peer Review Citing data in resear...
submit article and move on… publish article Research Environment Publication Environment Peer Review Standards for reprodu...
submit article and move on… publish article Research Environment Publication Environment Peer Review Hands On
Reproducible and citable data and models: an introduction.
Reproducible and citable data and models: an introduction.
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Reproducible and citable data and models: an introduction.

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Prepared and presented by Carole Goble (University of Manchester), Wolfgang Mueller (HITS), Dagmar Waltermath (University of Rostock), at the Reproducible and Citable Data and Models Workshop, Warnemünde, Germany. September 14th - 16th 2015.

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Reproducible and citable data and models: an introduction.

  1. 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. 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. 3. Reproducible Codes and Available Data
  4. 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. 5. FAIR Reproducibility Find, Access, Interoperate, Reuse
  6. 6. FAIR Publishing Catalogues Data specific Public Archives Commons & Cross Resource Infra Portable Packaging STANDARDS
  7. 7. Standards
  8. 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. 9. Citable Data • Persistent Identifiers • Resolution • Citation attribution • Credit lists • Citation infrastructure • Snapshots and versioning • Link Data with Publications
  10. 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. 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. 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. 13. submit article and move on… publish article Research Environment Publication Environment Peer Review Hands On

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