Curation of computational biology models Curation of computational biology models Anand Rampadarath & David Nickerson Anand Rampadarath & David Nickerson Auckland Bioengineering Institute, University of Aucklan a.rampadarath@auckland.ac.nz a.rampadarath@auckland.ac.nz https://reproduciblebiomodels.org/ https://reproduciblebiomodels.org/ d. d.nickerson@auckland.ac.nz ickerson@auckland.ac.nz
Acknowledgements Acknowledgements • Centre director: Herbert Sauro, University of Washington • Co-directors: – Jonathan Karr, Icahn School of Medicine at Mount Sinai – John Gennari, University of Washington – Ion Moraru, University of Connecticut Health • NIH/NIBIB Biomedical Technology Resource Center grant P41 EB023912 2 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Model curation service for journals Model curation service for journals Work with journals to improve reproducibility • Help develop common curation practices • – Domain specific vs general curation – Curation != validation Measuring reproducibility • – FAIR metrics and associated pitfalls Annotation • – Non-standard model formats – Simulation results 3 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Initial vision Initial vision 4 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
PLoS PLoSComp Biol Comp Biol - Pilot Pilot Author(s) submit manuscript Selected associate editors Existing submission pipeline Existing submission pipeline Suitable manuscripts Curation service checks reproducibility sent to curation service and produces reproducibility report (as a reviewer) Reproducibility report submitted as the “review” Editorial describing pilot: Editorial describing pilot: https ://doi.org/10.1371/journal.pcbi. https ://doi.org/10.1371/journal.pcbi. 1007881 1007881 5 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Reproducibility report Reproducibility report 6 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
PLoS PLoSComp Biol Comp Biol - Pilot Pilot ~70 submissions opt -in to pilot • ~40 reports submitted • 30% of submissions “reproducible” • At least one reported result could be reproduced – Common reasons we are unable to determine reproducibility • No code submitted or will be made available after acceptance – Missing data files – Software successfully installed and runs on test data, but no – mention of data used in paper Insufficient descriptions of how to use outputs to obtain results – Code provided without comments or documentation – 7 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Physiome Physiome • https://journal.physiom eproject.org • New journal with a focus on reproducibility • Reproducibility report included in publication • https://vph2020.sciencesconf.org/315725 8 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Reproducibility report Reproducibility report 9 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Reproducibility report Reproducibility report 10 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Reproducibility report Reproducibility report 11 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
Reproducibility report Reproducibility report 12 Slides available at https://doi.org/10.17608/k6.auckland.12871082 Slides available at https://doi.org/10.17608/k6.auckland.12871082
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