Public symposium of the BioHackathon 2019 will be held in Fukuoka on Sep 1st.
September 1st (Sun)
- 9:00 Registration opens
- Talks: From organizers
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| 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 |
| 14:15-14:20 | 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
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| 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
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| 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? |
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Yasunori Osana University of the Ryukyus, Japan
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- 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 |
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| 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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