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