Public symposium of the BioHackathon 2018 will be held at the Hotel Ichibata in Matsue on Dec 9th.

Note for speakers: Please try to leave few minutes for Q&A within a given slot (except for lightning talks).

December 9th (Sun)

  • 9:00 Registration opens
  • Talks: Resources
  • 10:00-10:20Introduction to the 11th NBDC/DBCLS BioHackathon & recap ELIXIR BH18
    Toshiaki Katayama Database Center for Life Science, Japan
    10:30-10:35FAIRness assessment for tools/software applications
    Leyla Jael Garcia Castro Elixir Hub
    10:35-10:40NBDC RDF portal 2018
    Shuichi Kawashima Database Center for Life Science (DBCLS), Japan
  • Talks: Biomedical
  • 10:40-10:50A single cell gene expression ontology (scOnto)
    Sebastian Burgstaller-Muehlbacher Max F Perutz Laboratories, Vienna Biocenter, Medical University of Vienna
    10:50-11:00Transcription factor ontology
    Yosuke Tanigawa Department of Biomedical Data Science, Stanford University (Stanford), U.S.A.
    11:00-11:10PhenoTips: helping doctors collect structured data to better diagnose genetic conditions
    Orion Buske Gene42, Canada
    11:10-11:20The RD-Connect Genome-Phenome Analysis Platform, for analysing, sharing, and solving rare disease cases
    Steven Laurie Centro Nacional de Analisis Genomico (CNAG-CRG), Barcelona, Spain
    11:20-11:30Structured Review and a Datascope Library: Surfing Waves of Knowledge Between BioThings
    Núria Queralt Rosinach Scripps Research (SR), USA
    11:30-11:35PubCaseFinder and PhenoTouch
    Toyofumi Fujiwara Database Center for Life Science (DBCLS), Japan
    11:35-11:40Nan-Byo diagnosis
    Giovanni Charles Mendelian
  • Talks: Agriculture
  • 11:40-11:50The Agronomic Linked Data project (AgroLD) a knowledge network platform for plants
    Pierre Larmande Institute of Research for Development (IRD)
    11:50-12:00Towards a Plant Breeding Ontology (PBO) enabling phenotypic and genotypic data interlinkage
    Erick Antezana Norwegian University of Science and Technology (NTNU), Norway and Bayer CropScience, Belgium
    12:00-12:05Hayai-Annotation Plants: R-package for an ultra fast and highly accurate gene annotation in plants
    Andrea Ghelfi Kazusa DNA Research Institute (KDRI), Japan
  • 12:05-13:30 Lunch
  • Talks: Omics
  • 13:30-13:40MetaNetX/MNXref: a resource for systems biology and metabolomics
    Marco Pagni SIB Swiss Institute of Bioinformatics, Switzerland
    13:40-13:50Knowledge graphs, applied use of terminologies, and improving the quality of linked content in the chemically-relevant biomedical research space
    Evan Bolton National Center for Biotechnology Information (NCBI), USA
    13:50-13:55Semantically linking glycoscience data in the GlyCosmos Portal
    Kiyoko F. Aoki-Kinoshita Soka University, Japan
    13:55-14:00The Carbohydrate-Active enZyme database
    Nicolas Terrapon Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université (AMU)
    14:00-14:05HAMAP rules
    Jerven Bolleman SIB Swiss Institute of Bioinformatics, Switzerland
    14:05-14:10jPOST proteome database (tentative)
    Susumu Goto Database Center for Life Science (DBCLS), Japan
    14:10-14:15All of gene expression (AOE)
    Hidemasa Bono Database Center for Life Science (DBCLS), Japan
    14:15-14:20Plasmid genomics
    Haruo Suzuki Keio University, Japan
    14:20-14:30Towards practical graphical pangenomics
    Erik Garrison Wellcome Trust Sanger Institute
    14:30-14:35Detection of small-size structural variants lethal in humans
    Vincenza Colonna National Research Council (CNR), Italy
    14:35-14:40MoMIG: a graph genome browser
    Toshiyuki Yokoyama The University of Tokyo, Japan
    14:40-14:45Personal data on genome graph
    Masanobu Jimbo WASEDA University, Japan
  • Talks: AMED
  • 14:45-14:55Enabling genomic & phenotypic data sharing for the benefit of human health
    Soichi Ogishima ToMMo, Tohoku Univ
    14:55-15:05Genome Medicine Alliance Japan (GEM-J): a proposal for GA4GH driver projects
    Takako Takai Japan Agency for Medical Research and Development (AMED)
    15:05-15:10MGeND: Integrated database of genomic and clinical information to promote precision medicine in Japan
    Mayumi Kamada Kyoto University, Japan
    15:10-15:15TogoVar: NBDC's integrated database of Japanese genomic variation
    Nobutaka Mitsuhashi National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST)
  • 15:15-16:30 Coffee break & exhibition
  • Talks: GA4GH
  • 16:30-16:40The GA4GH Cloud Work Stream: Emerging Standards for Genomics in the Cloud
    Brian Daniel O'Connor University of California Santa Cruz (UCSC)
  • Talks: Software
  • 16:40-16:50Enhanced data and tools use, re-use, and collaboration with the Common Workflow Language standards: from the life sciences to astrophysics and beyond.
    Michael R. Crusoe Common Workflow Language project (CWL)
    16:50-17:00Things that Docker does not provide for genome informatics
    Masahiro Kasahara University of Tokyo (UTokyo)
    17:00-17:05Where to run a workflow that runs wherever you want: runtime metrics analysis for workflow deployment
    Tazro Ohta Database Center for Life Science (DBCLS), Japan
    17:05-17:10Reproducible analysis challenge starts with software
    Pjotr Prins University Medical Center Utrecht, The Netherlands
    17:10-17:20mediKanren: a constraint logic language for biomedical reasoning
    William Edward Byrd Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, USA
    17:20-17:25KGX - a tool designed to exchange information for BioLink Model compliant KGs
    Deepak Raveendran Unni Lawrence Berkeley National Laboratory (LBNL)
    17:25-17:30Vec2SPARQL: combining SPARQL queries and vector space embeddings
    Maxat Kulmanov King Abdullah University of Science and Technology
    17:30-17:35Reduce Reuse Recycle in Data
    Yasunori Yamamoto Database Center for Life Science (DBCLS), Japan
    17:35-17:40Application of LOD Surfer to Multiple Protein Sequence Alignment
    Atsuko Yamaguchi Database Center for Life Science (DBCLS), Japan
    17:40-17:45Standardising BioJS components with WebComponents
    Yo Yehudi University of Cambridge
    17:45-17:50webcomponent to rdf integration
    Nobuyuki Aoki SparqLite LLC
    17:50-17:55TraitBLAST - towards a semantic framework for inter-species screening and comparison of phenotypes
    Claus Weiland Senckenberg Biodiversity and Climate Research Center (SBIK-F)
    Naohisa Goto Research Institute for Microbial Diseases (RIMD), Osaka University, Japan
    18:00-18:10Evaluating FAIRness
    Mark Wilkinson Center for Plant Biotechnology and Genomics, UPM Madrid
  • 18:15-18:30 Group photo
  • 19:00- Dinner

  • Live streaming will be available at