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Standardize experimental protocol description for reproducible science

Standardize experimental protocol description for reproducible science

Lightning Talk at NBDC/DBCLS Biohackathon 2017 at JST Science Plaza


Tazro Inutano Ohta

September 09, 2017


  1. Standardize experimental protocol description for reproducible science Tazro Ohta @inutano

    Database Center for Life Science BioHackathon 2017 Symposium
  2. Reproducibility: still problem from the slides of ISMB/ECCB 2013 Keynote

    by Prof. Carole Goble
  3. More reproduciblity = less humanity

  4. Experimental protocols for automation should be in a machine readable

    format without ambiguity executable by both machines and humans
  5. What we did #biohack14, #biohack15, #BLAH15, #biohack16, #BLAH16 Jean‑Luc, Alex,

    Olga, Erick, and me discussion and development of linked data model Protocols as Document Executable workflow Populating examples and use cases Collaboration with RBI, a company developing biological experiment automation robot Publication: Robotic crowd biology with Maholo LabDroids doi:10.1038/nbt.3758
  6. What we will do #biohack17 Brush up the model through

    populating examples Tranalation from existing protocols to linked data Human readable && Machine readable Write markdown, convert to linked data https://github.com/inutano/experimental‑protocols Biological sample to article figure in one click connect biological experiment to data analysis pipeline Common Workflow Language
  7. Team Pitagora‑Galaxy Reproducibility on data analysis "environment" SIG www.pitagora‑ galaxy.org

    Haruo Hiromu Manabu Masaaki Norio Ryota Tazro Yuh