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 opensTalks: Resources10:00-10:20 | Introduction to the 11th NBDC/DBCLS BioHackathon & recap ELIXIR BH18 | | Toshiaki Katayama Database Center for Life Science, Japan | 10:30-10:35 | FAIRness assessment for tools/software applications | | Leyla Jael Garcia Castro Elixir Hub | 10:35-10:40 | NBDC RDF portal 2018 | | Shuichi Kawashima Database Center for Life Science (DBCLS), Japan | Talks: Biomedical10:40-10:50 | A single cell gene expression ontology (scOnto) | | Sebastian Burgstaller-Muehlbacher Max F Perutz Laboratories, Vienna Biocenter, Medical University of Vienna | 10:50-11:00 | Transcription factor ontology | | Yosuke Tanigawa Department of Biomedical Data Science, Stanford University (Stanford), U.S.A. | 11:00-11:10 | PhenoTips: helping doctors collect structured data to better diagnose genetic conditions | | Orion Buske Gene42, Canada | 11:10-11:20 | The 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 | 11:20-11:30 | Structured Review and a Datascope Library: Surfing Waves of Knowledge Between BioThings | | Núria Queralt Rosinach Scripps Research (SR), USA | 11:30-11:35 | PubCaseFinder and PhenoTouch | | Toyofumi Fujiwara Database Center for Life Science (DBCLS), Japan | 11:35-11:40 | Nan-Byo diagnosis | | Giovanni Charles Mendelian | Talks: Agriculture11:40-11:50 | The Agronomic Linked Data project (AgroLD) a knowledge network platform for plants | | Pierre Larmande Institute of Research for Development (IRD) | 11:50-12:00 | Towards 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 | 12:00-12:05 | Hayai-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 LunchTalks: Omics13:30-13:40 | MetaNetX/MNXref: a resource for systems biology and metabolomics | | Marco Pagni SIB Swiss Institute of Bioinformatics, Switzerland | 13:40-13:50 | Knowledge 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 | 13:50-13:55 | Semantically linking glycoscience data in the GlyCosmos Portal | | Kiyoko F. Aoki-Kinoshita Soka University, Japan | 13:55-14:00 | The Carbohydrate-Active enZyme database | | Nicolas Terrapon Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université (AMU) | 14:00-14:05 | HAMAP rules | | Jerven Bolleman SIB Swiss Institute of Bioinformatics, Switzerland | 14:05-14:10 | jPOST proteome database (tentative) | | Susumu Goto Database Center for Life Science (DBCLS), Japan | 14:10-14:15 | All of gene expression (AOE) | | Hidemasa Bono Database Center for Life Science (DBCLS), Japan | 14:15-14:20 | Plasmid genomics | | Haruo Suzuki Keio University, Japan | 14:20-14:30 | Towards practical graphical pangenomics | | Erik Garrison Wellcome Trust Sanger Institute | 14:30-14:35 | Detection of small-size structural variants lethal in humans | | Vincenza Colonna National Research Council (CNR), Italy | 14:35-14:40 | MoMIG: a graph genome browser | | Toshiyuki Yokoyama The University of Tokyo, Japan | 14:40-14:45 | Personal data on genome graph | | Masanobu Jimbo WASEDA University, Japan | Talks: AMED14:45-14:55 | Enabling genomic & phenotypic data sharing for the benefit of human health | | Soichi Ogishima ToMMo, Tohoku Univ | 14:55-15:05 | Genome Medicine Alliance Japan (GEM-J): a proposal for GA4GH driver projects | | Takako Takai Japan Agency for Medical Research and Development (AMED) | 15:05-15:10 | MGeND: Integrated database of genomic and clinical information to promote precision medicine in Japan | | Mayumi Kamada Kyoto University, Japan | 15:10-15:15 | TogoVar: 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 & exhibitionTalks: GA4GH16:30-16:40 | The GA4GH Cloud Work Stream: Emerging Standards for Genomics in the Cloud | | Brian Daniel O'Connor University of California Santa Cruz (UCSC) | Talks: Software16:40-16:50 | Enhanced 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) | 16:50-17:00 | Things that Docker does not provide for genome informatics | | Masahiro Kasahara University of Tokyo (UTokyo) | 17:00-17:05 | Where to run a workflow that runs wherever you want: runtime metrics analysis for workflow deployment | | Tazro Ohta Database Center for Life Science (DBCLS), Japan | 17:05-17:10 | Reproducible analysis challenge starts with software | | Pjotr Prins University Medical Center Utrecht, The Netherlands | 17:10-17:20 | mediKanren: a constraint logic language for biomedical reasoning | | William Edward Byrd Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, USA | 17:20-17:25 | KGX - a tool designed to exchange information for BioLink Model compliant KGs | | Deepak Raveendran Unni Lawrence Berkeley National Laboratory (LBNL) | 17:25-17:30 | Vec2SPARQL: combining SPARQL queries and vector space embeddings | | Maxat Kulmanov King Abdullah University of Science and Technology | 17:30-17:35 | Reduce Reuse Recycle in Data | | Yasunori Yamamoto Database Center for Life Science (DBCLS), Japan | 17:35-17:40 | Application of LOD Surfer to Multiple Protein Sequence Alignment | | Atsuko Yamaguchi Database Center for Life Science (DBCLS), Japan | 17:40-17:45 | Standardising BioJS components with WebComponents | | Yo Yehudi University of Cambridge | 17:45-17:50 | webcomponent to rdf integration | | Nobuyuki Aoki SparqLite LLC | 17:50-17:55 | TraitBLAST - towards a semantic framework for inter-species screening and comparison of phenotypes | | Claus Weiland Senckenberg Biodiversity and Climate Research Center (SBIK-F) | 17:55-18:00 | BioRuby | | Naohisa Goto Research Institute for Microbial Diseases (RIMD), Osaka University, Japan | 18:00-18:10 | Evaluating FAIRness | | Mark Wilkinson Center for Plant Biotechnology and Genomics, UPM Madrid | 18:15-18:30 Group photo19:00- Dinner
Live streaming will be available at
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