BH19 symposium actual program
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Presenters: feel free to update your talk title and please make sure to link your slides by one day before the symposium day (Aug 31st)
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TimeActual timeFirst name
Family name
SlidesSymposium talk titleAffiliation
Requested symposium talk slot
Note
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From organizers
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10:0010:00SusumuGoto
https://docs.google.com/presentation/d/16ZTdSXLCd1YVpUCs-cOFMk3jp0P7O3Tj4WusTdSytDg/edit?usp=sharing
BioHackathon 2019: Welcome to FukuokaDatabase Center for Life Science (DBCLS), JapanLong talk
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10:08Announcement from Organizers
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10:1010:14ToshiakiKatayama
https://docs.google.com/presentation/d/1m7XX6AdORTGew6q1Fm0QVmYhbyrVzzD63cp08BkhRqg/edit?usp=sharing
Introduction to the BioHackathon 2019Database Center for Life Science (DBCLS), JapanLong talk
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RDF resources and applications
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10:2010:28JervenBolleman
https://drive.sib.swiss/index.php/s/Dg7pw5XMprM2tNG
SPARQLing Science for dull budgetsSIB Swiss Institute of Bioinformatics, SwitzerlandLong talk
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10:3010:40SimonJupp
https://drive.google.com/file/d/1ufqlUJz6vNk3sMQZ4YAJGVD6GCFcJa9w/view?usp=sharing
Approaches to developing “RDF friendly” metadata standards European Bioinformatics Institute (EMBL-EBI)Long talk
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10:5010:50ChrisMungall
https://drive.google.com/file/d/1-fAki3JWdJO0NTmtugJSEUbAG1R8NO1O/view
SparqlProg - Logic Programs for the Biological Semantic WebLawrence Berkeley National LaboratoryLong talk
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10:4011:01EvanBolton
https://ftp.ncbi.nlm.nih.gov/pubchem/.bh2019/Biohackaton%202019.pptx
Towards improving the data ecosystem for scientists
National Center for Biotechnology Information (NCBI), USA
Long talk
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11:0011:13JulienMariethoz
https://docs.google.com/presentation/d/1WaiuCR83bq8bnxBoD-QapZLNosX89L6q4NBM5fXyETA/edit?usp=sharing
Semantically connecting GlycoProteins with SPARQLy visualizationsSwiss Institute of Bioinformatics (SIB), SwitzerlandLightning talk
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11:0511:19ErickAntezana
https://drive.google.com/open?id=1Y7NJ5DDbS8bsptJmpvxDG_oVYFr0XaeN
Network building with the BioGateway App.
Norwegian University of Science and Technology, Norway & Bayer CropScience, Belgium
Lightning talk
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11:1011:23OrionBuske
https://docs.google.com/presentation/d/1X8qAR5TEMn6PU8x6imlafwtVSoLpOkr2jxJWh7oPv70/edit?usp=sharing
Data sharing services for genomic medicinePhenoTips/Gene42Lightning talk
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FAIR
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11:1511:29MichelDumontier
https://docs.google.com/presentation/d/1LwSFDd8cFKMc20K_tMvrAy4Fhg3LwvB1BV3leQoOApw/edit?usp=sharing
Analyzing partitioned FAIR health data responsiblyMaastricht University, NetherlandsLong talk
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11:2511:36ChunleiWu
https://docs.google.com/presentation/d/1qkoKOl7ifeAKGQmw_CAt7p79zSdfRZWh9bEUk13hyEY/edit?usp=sharing
Schema Playground: prompting FAIR schemas to support FAIR dataScripps ResearchLong talk
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11:35 11:46Alexander
Garcia Castro
https://docs.google.com/presentation/d/1c4eSbTbaJ2ydEujvL1AA1rWghVFesy__nEtRIZeI-kA/edit?usp=sharing
The Journal of Research Objects, to be born FAIR for a journal.BASFLong talk
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11:4511:57Q&A
https://app.sli.do/event/a5nxxdnm/live/questions
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12:00
Group photo
link to photo please!
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12:15-14:00
Lunch break
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RDF resources developed in Japan
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14:0014:01MayumiKamada
https://drive.google.com/file/d/130a2v2-fML_3UWlBa8R2001gOyU6R9ew/view?usp=sharing
Med2RDF project for biomedical data integrationKyoto UniveristyLightning talk
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14:0514:07TakeyaKasukawa
https://drive.google.com/file/d/18USnAb6bruy4IIsuAmVbDri-QhCEdaGx/view
FANTOM and refTSS promoter resources
RIKEN Center for Integrative Medical Sciences (IMS), Japan
Long talk
Arriving at FUK 9:20AM
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14:1014:13HidemasaBono
https://drive.google.com/file/d/15q7qoMxlLfWRxMHcw9AxBkvhHQVb65v6/view?usp=sharing
TogoEx: the integration of gene expression dataDatabase Center for Life Science (DBCLS)Lightning talk
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14:1514:19SusumuGoto
https://drive.google.com/file/d/1VJSIRcypOu6RoO6sNXOMjCxBS2H_FMup/view?usp=sharing
jPOST environment for proteome dataDatabase Center for Life Science (DBCLS), JapanLightning talk
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14:2014:24ChihiroHiguchi
https://drive.google.com/file/d/19oK4JlmvGM9biDdJpkFOZkGTaJdxOTxI/view?usp=sharin)g
DruMAP RDF Pharmacokinetics database to RDF
National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Laboratory of Bioinformatics
Lightning talk
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14:2514:29SatoshiKume
https://drive.google.com/file/d/18iAnym5wmzI8a2IKLElmXvUaRhHr-a41/view?usp=sharing
Semantic Segmentation for Image Metadata Creation in Imaging Metadatabase
RIKEN Center for Biosystems Dynamics Research (RIKEN BDR)
Lightning talk
30
Data analysis and machine learning
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14:3014:35WilliamByrd
https://docs.google.com/presentation/d/1bnD34kGPFsYmjIjN33evl1EchdJwSNRale26t7B8eig/edit?usp=sharing
Functional and relational programming for biology and medicine - or, miniKanren meets SPARQL/SPARQPROG
Hugh Kaul Precision Medicine Institute/Computer Science, University of Alabama at Birmingham, USA
Long talk
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14:4014:46Pier LuigiButtigieg
https://owncloud.mpi-bremen.de/index.php/s/WnVI5GJxWOuYJ8u
Going cosmic: Bridging planetary and life science semantics through hackathons
Alfred Wegener Institute (AWI), GermanyLong talk
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14:5014:57ClausWeilandhttps://bit.ly/2NAcYFcBridging the gap between bio* knowledge graphs and machine learning
Senckenberg Biodiversity and Climate Research Centre (SBIK-F)
Long talk
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15:1015:07RobertHoehndorf
http://leechuck.de/biohackathon2019.pdf
Instrastructure for combining ontologies, Linked Data, and machine learningKing Abdullah University of Science and TechnologyLightning talk
Arriving at FUK 7:00AM
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15:2015:12ThomasLiener
https://docs.google.com/presentation/d/1K-pWPnSkK7avYeLOPc6LqyoiEeJE6ViDoL5Tdlm9lgw/edit?usp=sharing
Human readable RDF validationNoneLightning talk
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15:2515:17Jose EmilioLabra Gayo
https://docs.google.com/presentation/d/1dLu6t35MzUCLwUO01hHeNzHpuSzpHSj31lTtbLSxIzU/edit?usp=sharing
Data models, visualizations and Shape Expressions for RDFUniversity of Oviedo, SpainLightning talk
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15:3015:23Leyla
Garcia Castro
https://drive.google.com/file/d/10E7e2-i1IZXR8Nq6GLp8FLtcx_grxboC/view?usp=sharing
Bioschemas validator
ZBMED Information Centre for Life Sciences, Germany
Lightning talk
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15:3515:27DeepakUnni
https://docs.google.com/presentation/d/1zKS2D-lSNmLQ-1cDyVDhHLnc7E6PWlp7WKFOE-ykM_k/edit?usp=sharing
BioLink Model - standardizing knowledge graphs and making them interoperable
Lawrence Berkeley National Laboratory (LBNL)Lightning talk
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15:4015:33YasunoriYamamoto
https://docs.google.com/presentation/d/1hAzKnLdG_5cQDHkjqppqN5ULQDRSbNy3pM2Tb7mhpPA/edit?usp=sharing
Keep data accessible, reliable, and greatDatabase Center for Life Science (DBCLS), JapanLightning talk
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15:4515:39Q&A
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15:45-16:15
Coffee break
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> 16:15-17:00
Services and tools
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16:1516:17MasahiroKasahara
https://www.dropbox.com/s/mztb9i6wrnjayvv/201909019BioH2019.pptx?dl=0
Making genomics workflows truly portableThe University of TokyoLong talk
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16:2516:27HirotakaSuetake
https://docs.google.com/presentation/d/1YRKCM1KwHyNOz7B6AP2j5qIHjl7Ew9CnAtvXA1xSeNY/preview
SAPPORO & tonkaz: Test framework for data analysisThe University of TokyoLong talk
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16:3516:35MichaelCrusoehttps://tinyurl.com/2019-CWL-biohack19Common Workflow Language standards: v1.1 and beyond!
Common Workflow Language (CWL) project & ELIXIR-Netherlands
Lightning talk
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16:4016:41AlexanderKanitz
https://docs.google.com/presentation/d/17sLndD66nESHMXJhQZ2m4mxwFvMd0lZgTwjBOmFn8J0/preview
WES-ELIXIR - A language-agnostic implementation of the GA4GH Workflow Execution Service API
Swiss Institute of Bioinformatics (SIB) / ELIXIR Switzerland
Lightning talk
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16:4516:46NaohisaGoto
https://drive.google.com/file/d/1-_uaT6q9IiaGi4qWj5Xo506vCRs7uCmO/view?usp=sharing
BioRuby 2.0RIMD, Osaka University, JapanLightning talk
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16:5016:51KozoNishida
https://docs.google.com/presentation/d/1ycSkiNcCQxuRj1nGkziq48GZFJo5GCSoEN_uDqvq2Gc/edit?usp=sharing
Dashboarding pathway network with Dash-CytoscapeRIKENLightning talk
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16:5516:56YasunoriOsana
https://lut.eee.u-ryukyu.ac.jp/owncloud/index.php/s/Odn4i44uqOV6EDf
FPGA acceleration: any opportunity in Bioinformatics?University of the Ryukyus, JapanLightning talk
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> 17:00-17:50
Genome graph and visualization
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17:0017:01ErikGarrison
https://docs.google.com/presentation/d/10KDUnRJyKwi5q9khCcb0C9Mb52XcGZbfvFFF0nNCbGg/edit?usp=sharing
Untangling the pangenomeUniversity of California, Santa Cruz (UCSC) USALong talk
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17:1017:11SimonHeumos
https://docs.google.com/presentation/d/1FFj0-10Sd3hyLajb_d8oDXDLEGDWEgwuYSmoZ8W9vyQ/edit?usp=sharing
Interactive Visualization of Genome Variation GraphsQuantitative Biology Center (QBiC), GermanyLong talk
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17:2017:21JosiahSeaman
https://docs.google.com/presentation/d/1GD_-OAlh-x-JyDeB-br-cynOgJXpFJquw0Ir2KT3Hdc/edit?usp=drivesdk
Summarizing Graph Genomes to Capture True Species DiversityRoyal Botanic Gardens KewLong talk
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17:3017:31ToshiyukiYokoyama
https://docs.google.com/presentation/d/1tjqs83_eDXVyeSD_UPi5r8JuG8VCR_-JAAPRIquh-38/edit?usp=sharing
Visualization and Application of Graph GenomesThe University of TokyoLightning talk
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17:3517:37ChristianFischerhttps://chfi.github.io/bh2019/slides.htmlGenetics Browser & VG visualisation
University of Tennessee Health Science Center (UTHSC)
Lightning talk
Arriving at FUK 9:45AM
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17:4017:41JouniSirén
https://docs.google.com/presentation/d/1GYgeiVC8siyHaTAIktfj-UFLueBbvtSTkrYzjKJ21cE/edit?usp=sharing
GBWTGraphUniversity of California Santa Cruz (UCSC)Lightning talk
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17:4517:46PjotrPrinshttp://biogems.info/bh12.pdfThe great data mashup
University of Tennessee Health Science Center (UTHSC), USA
Lightning talk
Arriving at FUK 9:45AM
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> 17:50-18:20
contd. Data analysis and machine learning (due to flight delay)
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17:5017:54MonaAlshahrani
https://drive.google.com/file/d/1bb6QoZGNaD-dqg2dI2BOx9awYQGPZBvK/view?usp=sharing
Knowledge graph representation learning: approaches and applications in biomedicine
King Abdullah University of Science and Technology (KAUST), Saudi Arabia
Long talk
Will be postponed to the other day due to flight delay
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18:0018:07MaxatKulmanov
https://www.dropbox.com/s/bc65up7qfwnryme/deepgoplus.pdf?dl=1
DeepGOPlus: Improved protein function prediction from sequence
King Abdullah University of Science and Technology (KAUST)
Lightning talk
Will be postponed to the other day due to flight delay
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18:0518:13Q&A
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Collaboration with the ELIXIR BH
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18:2018:18Victoria
Dominguez del Angel
https://docs.google.com/presentation/d/1I8F5TOAWDBlWsiVyNlRGF048wFyazevM/present?token=AC4w5Vg8bklUeQuttsUvqWMvI9xY7IhnUg%3A1567266564845&includes_info_params=1&eisi=CPCZ9_a6reQCFQTzJAodfzMNNQ#slide=id.p1
Elixir-Europe BiohackathonInstitut Français de Bioinformatique, ELIXIR-FRLightning talk
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18:2518:24
Announcements from organizers
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Enjoy Fukuoka night
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Flight delay
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Tomorrow?(5min)GarrettStevens
https://docs.google.com/presentation/d/1IFmTDbRyFz_TfpBm10vdNUUKMakeYwGXFW34FIW9AsM/edit?usp=sharing
JBrowse 2: Genome browsing for the modern webUniversity of California Berkeley (UC Berkeley), USALightning talk
Will be postponed to the other day due to flight delay
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