Symposium

Public symposium of the BioHackathon 2019 will be held in Fukuoka on Sep 1st.

September 1st (Sun)

  • 9:00 Registration opens
  • Talks: From organizers
  • 10:00-10:10 BioHackathon 2019: Welcome to Fukuoka
    Susumu Goto Database Center for Life Science (DBCLS), Japan
    10:10-10:20 Introduction to the 12th NBDC/DBCLS BioHackathon
    Toshiaki Katayama Database Center for Life Science(DBCLS), Japan
  • Talks: RDF resources and applications
  • 10:20-10:30 SPARQLing Science for dull budgets
    Jerven Bolleman Swiss Institute of Bioinformatics (SIB), Switzerland
    10:30-10:40 Approaches to developing “RDF friendly” metadata standards
    Simon Jupp     European Bioinformatics Institute (EMBL-EBI), UK
    10:40-10:50 SparqlProg - Logic Programs for the Biological Semantic Web
    Chris Mungall Lawrence Berkeley National Laboratory (LBNL), USA
    10:50-11:00 Towards improving the data ecosystem for scientists
    Evan Bolton     National Center for Biotechnology Information (NCBI), USA
    11:00-11:05 Semantically connecting GlycoProteins with SPARQLy visualizations
    Julien Mariethoz Swiss Institute of Bioinformatics (SIB), Switzerland
    11:05-11:10 Network building with the BioGateway App.
    Erick Antezana     Norwegian University of Science and Technology, Norway & Bayer CropScience, Belgium
    11:10-11:15 Data sharing services for genomic medicine
    Orion Buske PhenoTips/Gene42, Canada
  • Talks: FAIR
  • 11:15-11:25 Analyzing partitioned FAIR health data responsibly
    Michel Dumontier Maastricht University, Netherlands
    11:25-11 :35 Schema Playground: prompting FAIR schemas to support FAIR data
    Chunlei Wu Scripps Research, USA
    11:35-11:45 The Journal of Research Objects, to be born FAIR for a journal.
    Alexander Garcia Castro BASF, Spain
  • 11:45-12:00 Q&A
  • 12:00 Group photo
  • 12:15-14:00 Lunch break (outside of the building, in the city center)
  • Talks: RDF resources developed in Japan
  • 14:00-14:05 Med2RDF project for biomedical data integration
    Mayumi Kamada Kyoto Univeristy, Japan
    14:05-14:10 FANTOM and refTSS promoter resources
    Takeya Kusukawa RIKEN Center for Integrative Medical Sciences (IMS), Japan
    14:10-14:15 TogoEx: the integration of gene expression data
    Hidemasa Bono Database Center for Life Science (DBCLS), Japan
    14:15-1 4:20 jPOST environment for proteome data
    Susumu Goto Database Center for Life Science (DBCLS), Japan
    14:20-14:25 DruMAP RDF Pharmacokinetics database to RDF
    Chihiro Higuchi National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Laboratory of Bioinformatics, Japan
    14:25-14:30 Semantic Segmentation for Image Metadata Creation in RIKEN Imaging Metadatabase
    Satoshi Kume RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Jspan
  • Talks: Data analysis and machine learning
  • 14:30-14:40 Hayai Domain Architecture Matching for protein identification
    William Byrd Hugh Kaul Precision Medicine Institute/Computer Science, University of Alabama at Birmingham, USA
    14:40-14:50 Going cosmic: Semantic hackathons to bridge planetary and life science data and communities
    Pier Luigi Buttigieg Alfred Wegener Institute (AWI), Germany
    14:50-15:00 Bridging the gap between bio* knowledge graphs and machine learning
    Claus Weiland Senckenberg Biodiversity and Climate Research Centre (SBIK-F) , Germany
    15:00-15:05 Linked Data, Ontologies, and Learning A new paradigm for working with biological data
    Robert Hoehndorf King Abdullah University of Science and Technology (KAUST), Saudi Arabia
    15:05-15:10 Human readable RDF validation
    Tomas Liener
    15:10-15:15 Data models, visualizations and Shape Expressions for RDF
    Jose Emilio Labra Gayo University of Oviedo, Spain
    15:15-15:20 Bioschemas validator
    Leyla Garcia Castro ZBMED Information Centre for Life Sciences, Germany
    15:20-15:25 BioLink Model - standardizing knowledge graphs and making them interoperable
    Deepak Unni Lawrence Berkeley National Laboratory (LBNL), USA
    15:25-15:30 Umaka Yummy Data Suite
    Yasunori Yamamoto Database Center for Life Science (DBCLS), Japan
  • 15:30-15:45 Q&A
  • 15:45-16:15 Coffee break
  • Talks: Services and tools
  • 16:15-16:25 Making genomics workflows truly portable
    Masahiro Kasahara The University of Tokyo, Japan
    16:25-16:35 SAPPORO & tonkaz: Test framework for data analysis
    Hirotaka Suetake The University of Tokyo, Japan
    16:35-16:40 Common Workflow Language standards: v1.1 and beyond!
    Michael Crusoe Common Workflow Language (CWL) project & ELIXIR-Netherlands, Netherlands
    16:40-16:45 WES-ELIXIR - A language-agnostic implementation of the GA4GH Workflow Execution Service API
    Alexander Kanitz Swiss Institute of Bioinformatics (SIB) / ELIXIR Switzerland, Switzerland
    16:45-16:50 BioRuby 2.0
    Naohisa Goto RIMD, Osaka University, Japan
    16:50-16:55 Dashboarding pathway network with Dash-Cytoscape
    Kozo Nishida RIKEN, Japan
    16:55-17:00 FPGA acceleration: any opportunity in Bioinformatics?
    Yasunori Osana University of the Ryukyus, Japan
  • Talks: Genome graph and visualization
  • 17:00-17:10 Untangling the pangenome
    Erik Garrison University of California, Santa Cruz (UCSC), USA
    17:10-17:20 VG Browser: Interactive Visualization of Genome Variation Graphs
    Simon Heumos Quantitative Biology Center (QBiC), Germany
    17:20-17:30 VG Browser: Summarizing Graph Genomes
    Josiah Seaman Royal Botanic Gardens Kew, UK
    17:30-17:35 Visualization and Application of Graph Genomes
    Toshiyuki Yokoyama The University of Tokyo, Japan
    17:35-17:40 Genetics Browser & Variant Graph Visualization
    Jens Fischer University of Tennessee Health Science Center (UTHSC), USA
    17:40-17:45 GBWTGraph
    Jouni Sirén University of California, Santa Cruz (UCSC), USA
    17:45-17:50 The great data mashup
    Pjotr Prins University of Tennessee Health Science Center (UTHSC), USA
    xx:xx-xx:xx (will be postponed to the other day due to flight delay) JBrowse 2: Genome browsing for the modern web
    Garrett Stevens University of California Berkeley (UC Berkeley), USA
  • Talks: contd. Data analysis and machine learning (due to flight delay)
  • 17:50-18:00 Knowledge graph representation learning: approaches and applications in biomedicine
    Mona Alshahrani King Abdullah University of Science and Technology (KAUST), Saudi Arabia
    18:00-18:05 DeepGOPlus: Improved protein function prediction from sequence
    Maxat Kulmanov King Abdullah University of Science and Technology (KAUST), Saudi Arabia
  • 18:05-18:20 Q&A
  • Talks: Collaboration with the ELIXER BH
  • 18:20-18:25 Elixir-Europe Biohackathon 2019
    Victoria Dominguez del Angel Institut Français de Bioinformatique, ELIXIR-FR, France
  • 18:25 Announcements from organizers
  • 18:30 Closing

Live streaming will be available at
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