BioHackathon 2023

Workshop

Self-introduction

Tem Plate

Fixme University, Japan

• Background/Skills
• Briefly describe your professional works or products
• Ideas for this hackathon
• What you plan to start with for the [R1], [R2], [R3], or [R4]
• Favorite programming language: ???
• Things to share
• Please provide a brief message that encapsulates your distinctive personality memorably, e.g.,
• What no one else on earth but you do
• The happiest thing happened in my life
• Your recent updates

​

[R1], [T2], [T3]

Research interest

Pre-defined target domains for BioHackaton 2023

• [R1] Multi-omics analysis on human genotype to phenotype that includes genomic, transcriptomic, epigenomic, proteomic, protein structures, and biochemical data.
• [R2] Automated data analysis of microorganisms including phylogenetic compositions, gene annotations, pathways, and growth conditions.
• [R3] Data-driven interdisciplinary studies in public health, environment, agriculture, food, energy, and other fields.
• [R4] Facilitating knowledge discovery and biological analysis of knowledge graphs and literature.
• If you choose [R4], please indicate to which project from [R1], [R2], or [R3] your outcome will contribute most.

​

Technical aspects

Pick up your technical expertise

• [T1] Data
• [T2] Algorithm
• [T3] Analysis
• [T4] Tool
• [T5] Application
• [T6] Workflow

​

Toshiaki Katayama

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Database and tool development (Togo*, RDF-config etc.)
• Ideas for this hackathon
• Standardize a data model for long-read-based structural variations (SVs) with pangenome and explore analysis pipelines for my genome
• Favorite programming language: Ruby
• Things to share
• Tasted (not visited;) Japanese sake from 600 breweries

[R4] (will contribute to [R1]), [T1], [T4]

Tazro Ohta

Chiba University, Japan

• Background/Skills
• Informatics person in a lab called “AI Medicine”
• Ideas for this hackathon
• Standardize sample metadata by LLM to automate data analysis
• Favorite programming language: awk
• Things to share
• Left DBCLS this March, new challenge in Chiba-U!
• My Team won the 2022-2023 season of Italian football league after a 33-year wait (Fig.1)

[R1], [T1], [T3], [T4], [T5], [T6]

Fig. 1: Me screaming at the stadium celebrating the historical league win (May 7 2023, Naples, Italy)

Shuichi Kawashima

​

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• RDF portal, TogoMedium etc.
• Ideas for this hackathon
• Develop microbial pathway data in RDF and visualize them
• Collaborate with other microbiology research groups (MicrobiomeDataHub, NBRC etc..)
• Favorite programming language: Ruby
• Things to share
• happy to host the first international BioHackathon Japan in four years!

[R1], [T1], [T5]

Hiromasa Ono

​

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Editor in chief & producer @ TogoTV 📺
• A video archive for how to use bioinformatics tools and DBs
• Developer @ RefEx 📊
• A webtool to easily search and view the gene expression data
• Ideas for this hackathon
• [R1]: Utilize reference gene expression datasets to help with �biological interpretation of omics data analysis
• Favorite programming language: shell, R
• Things to share
• if you have DBs or tools that would be better to make a how-to video, please let me know!😁
• A horse lover 🐴🐎

[R1], [T1], [T5]

Terue Takatsuki

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• I work on ontology-related work.(BRSO, NANDO, MP-Japanese…)
• Ideas for this hackathon
• I work for all participates as help desk staff.
• Favorite programming language: ???
• Things to share
• I am happy that everyone can enjoy the hackathon,no issues and problems.
• If you need help except “hacking”, please let us know.

​

[R3], [T1]

Mark D Wilkinson

Universidad Politécnica de Madrid

• Background/Skills
• FAIR Advocate, Linked Data, Data integration
• Ideas for this hackathon
• Open Digital Rights Language “negotiator”
• Modelling of exemplar data requests in ODRL
• “Triage” against ODRL-modelled �consent/policy statements
• Draft portions of Nagoya Protocol in ODRL
• Favorite programming language: Be-ru
• Things to share
• Married for 2 months - so far so good
• I made the wedding dress myself!
• Started my career studying flowers

​

[R3], [T4], [T5]

Gmihail at Serbian Wikipedia.

Alberto Labarga

Barcelona Supercomputing Center (BSC-CNS), Spain

• Background/Skills
• EHR interoperability, NLP, OMOP-CDM, GA4GH tools (beacon, cryptGH), EGA
• Ideas for this hackathon
• Knowledge graph automatic extraction from clinical data using LLMs
• Multi-omics data integration using deep learning
• Favorite programming language: Python
• Things to share
• I have run with bulls

[R4] (will contribute to [R1]), [T1], [T3]

Hiroshi Mori

​

National Institute of Genetics, Japan

• Background/Skills
• Microbiology, Metagenome-informatics
• DBs: MicrobeDB.jp, Microbiome Datahub
• Ideas for this hackathon
• Develop microbial metadata (e.g., BioSample, strain description) auto-cleaning and annotation program
• Favorite programming language: Perl, R, Python
• Things to share
• sequencing and analysing SARS-CoV-2 genomes every week (since May 2021)
• Recruiting Postdocs (microbiome DB development, genome-informatics)

[R2], [T1], [T3]

Yuki Moriya

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Development DBs & tools
• SPARQL support, Endpoint browser, Togo*, jPOSTdb etc.
• Ideas for this hackathon
• Data construction and visualization of microbial pathways
• Favorite programming language: sparql, perl
• Things to share
• Please enjoy Japanese sake in Kagawa selected by the organizers

​

[R2], [T1], [T4], [T5]

Hirokazu Chiba

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Data processing & DB construction (including RDF)
• Omics data analysis, including cross-species comparison on the basis of orthology relations
• Ideas for this hackathon
• Contribute to the data processing for databases of human genes
• Comparative sequence analysis especially of non-coding regions
• Favorite programming language: Perl, JavaScript, (Python, C)
• Things to share
• I live in Chiba now, but my hometown is different, in Ibaraki prefecture (where this photo is taken).

​

[R1], [T1], [T3], [T4]

Shuya Ikeda

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• TogoID: ID conversion tool covering various kinds of�biological DBs
• Ideas for this hackathon
• Adding ID pairs necessary for database integration to TogoID
• Favorite programming language: awk
• Things to share
• Love spiders

​

[R1], [T1], [T3]

Hidemasa Bono

​

Hiroshima University Genome Editing Innovation Center, Japan

• Background/Skills
• Initiator for TogoTV, RefEx & FANTOM
• Bioinformatics teacher at Hiroshima University
• A PI for the center of innovation for BioDX, COI-NEXT
• Ideas for this hackathon
• In collaboration with WikiPathways team headed by Dr. Alex Pico from UCSF, we will expand the pathway analysis environment to non-model organisms where genome and functional annotations are not organized in the central public database.
• Favorite programming language: shell scripts, Perl
• Things to share
• I will be at BH23 during Jun 25 - 28

[R3], [T1], [T3], [T6]

Michael R. Crusoe

ELIXIR-Germany / Freie Universität Berlin, Germany

• Background/Skills
• Co-founder, Common Workflow Language project & CWL project lead
• Ideas for this hackathon
• Improving the Bio* CWL tool repository
• Work with Tomoya Tanjo and others on CWL v1.3 proposals
• Help Erik Garrison with auto-selecting optimized binaries
• Meet people and learn from them!
• Favorite programming languages: Python (and Common Workflow Language!)
• Things to share:
• Still can’t speak German. I hope to defend my PhD in the next 6-9 months!
• My American friend, Russell Neches, is a new Assistant Professor at Kyoto University in the Ogata Laboratory; please contact him if you are interested in asking basic questions about evolution, particularly phylogenetic methods

[R1+], [T6]

Jerven Bolleman

Swiss Institute of Bioinformatics, Switzerland

• Background/Skills
• UniProt, Rhea, SwissLipids and so much SPARQL
• Ideas for this hackathon
• Improving the linkage between RDF wwPDB and the chemical world and so via a secondary route to UniProtKB and Rhea. To better explore the natural and unnatural ligands in UniProtKB.
• Favorite programming language: SPARQL, JAVA
• Things to share
• Implementing storage engines for SPARQL is very enjoyable
• Fan of anything SPARQLing: champagne, methode traditionelle, sake
• Exception to the rule: water ;)

​

[R1], [T1], [T5]

Evan Bolton

National Center for Biotechnology Information, USA

• Background/Skills
• Anything PubChem, chemical informatics, biomedical data
• Ideas for this hackathon
• Making major advances in glycoinformatics data linking, sharing, and harmonization.
• Favorite programming language: PERL, C++
• Things to share
• Team-lead with the PubChem project since its inception 19 years ago
• This will be my seventh time attending the DBCLS Biohackathon
• Chat with me about PubChemRDF :-D

[R1], [R2], [R3], [R4], [T1], [T2], [T3], [T4], [T5], [T6]

Jose Emilio Labra Gayo

WESO Research Group, University of Oviedo, Spain

• Background/Skills
• ShEx, SPARQL, RDF
• Ideas for this hackathon
• Subsets/integrations of large RDF datasets
• Implement new ShEx validator/subset extractor in Rust
• Favorite programming language: RUST, Scala, Haskell
• Things to share
• Implemented ShEx validators and Wikidata subsetting tools in Scala
• Semantic web researcher since 2004
• Phd about programming language design in 2001
• Second time attending DBCLS hackathon

​

[R4] (will contribute to [R3]), [T1], [T2], [T4], [T5]

Naoya Oishi

Dogrun Inc. , Japan

• Background/Skills
• Creating data exploration and visualization tools.
• Ideas for this hackathon
• To acquire a more appropriate pathway notation for describing genes, enzymes, and metabolites in GPML.
• The concept of database configuration and application for pathway data exploration will be discussed.
• Favorite programming language: Python
• Things to share
• ​

​

[R3], [T5]

Hideya Kawaji

Tokyo Metropolitan Institute of Medical Science, Japan

• Background/Skills
• Lead of the FANTOM5 web resource and D3G
• Co-lead of http://fanta.bio
• Co-operate running the Asian mirror of the UCSC Genome Browser
• Ideas for this hackathon
• Explore use of more genomics data with transcriptome-based annotations
• Align useful resource/annotations based on trackhub
• Favorite programming language:
• shell (bash), awk, ruby, R
• Things to share
• My last visit to BH was in 2017. I moved to TMiMS from RIKEN in 2019.
• I’ll be BH2023 in June 25 to 27 (morning).
• We are hiring! Contact me if you are interested in.

[R1], [T1], [T2], [T3], [T4], [T5]

Erick Antezana

UN-International Computing Center, Spain

• Background/Skills
• BioGateway, Data Governance, Ag. Data standardisation
• Ideas for this hackathon
• Linked Data Governance: principles, metrics
• AI Governance
• Favorite programming language: PERL / C++
• Things to share
• Participated in ten BHs (Japan)
• My wish: organise a BH in Bolivia
• Your recent updates: transition to a new job/role

​

[R4] (focus on [R3]), [T1], [T4], [T5]

Takeya Kasukawa

RIKEN Center for Integrative Medical Sciences, Japan

• Background/Skills
• Informatics: database, data engineering, IT infra
• Biology: transcriptional regulation, transcriptome (bulk/single-cell)
• Contributing DBs: FANTOM, INTRARED, fanta.bio, …
• Ideas for this hackathon
• Association of genomic elements (CREs) with phenotypes/diseases
• Favorite programming language: Perl, R, shell, make
• Things to share
• Attending: June 25 (Sun) to June 27 (Tue)
• Experiencing data coordination in the large-scale data production proj.
• Having experiences in the long-term operations of biomedical databases

​

[R1], [T1], [T3], [T6]

Nishad Thalhath

RIKEN Center for Integrative Medical Sciences, Japan

• Background/Skills
• Research interests in Semantic Interoperability.
• Acquiring working knowledge in approaches and perspectives based on Information Science.
• Ideas for this hackathon
• Exploring the possibilities of developing semantically enriched data production workflows for stakeholders.
• Favorite programming language: I know some OCaml, and I am also trying to learn other programming languages.
• Things to share
• My native language is Malayalam, which is a palindrome noun in English.
• I have very minimal knowledge in the fields of life-science and 'omics'.

R4 (Contributes to R1 & R3) - T4, T5, T6

Teemu Kataja

CSC - IT Center for Science, Finland

• Background/Skills
• Backend development, system integrations, web apps, APIs
• CLI/GUI tools, automation, pipelines
• Ideas for this hackathon
• Methods of describing datasets to increase discoverability, interoperability, and reusability (FAIR principles)
• Favorite programming language: Go
• Things to share
• This is my first (bio)hackathon ever, I’m excited! :D
• I recently started learning to play the piano as a hobby
• Finnish and Japanese pronunciation is very similar, if you change the “J” to “Y” in my last name, you get the correct sound: テーム カタヤ

​

[R4] + [R1], [T4], [T5], [T6]

Alex Kanitz

Swiss Institute of Bioinformatics, Switzerland

• Background/Skills
• Web dev, GA4GH APIs, workflows, bit of DevOps
• “Product”: ELIXIR Cloud
• Ideas for this hackathon
• Set up a FAIR #biohackathon-cloud infrastructure to�support projects for this & future BioHackathons�⇒ Please reach out with any use cases you may have 🙌
• Favorite programming language: Commodore BASIC 😉 / 🐍
• Things to share
• Won 2006 Singapore National Baseball League�⇒ First collaboration with

[R1], [T3], [T4], [T5], [T6]

Mori

Takeru Nakazato

National Institute of Technology and Evaluation (NITE), Japan

• Background/Skills
• Biological Resource Center, NITE (NBRC) provides�Microbial resources and information.
• Database, Gene annotation, Knowledge extraction from PubMed
• Ideas for this hackathon
• Standardization of strain information such as culture conditions and sampling
• Linking data in different microbial culture collections and databases
• Favorite programming language: Perl, Python
• Things to share
• Job change from DBCLS to NBRC, NITE (June 2022)
• Biodiversity Information Standards (TDWG) member
• I plan to do insect sampling on Shodoshima. I hope it doesn't rain...

​

[R2], [T1], [T4], [T5]

Risa Otsuka

National Institute of Technology and Evaluation (NITE), Japan

• Background/Skills
• Biological Resource Center, NITE (NBRC) provides�Microbial resources and information.
• DBRP (Data and BiologicalResources Platform)
• Programmer, data visualize, data convertion tool
• Ideas for this hackathon
• Search microbial data from various options
• Favorite programming language: JavaScript, Python
• Things to share
• I love music (listening, playing the violin and viola)

​

[R2], [T1], [T4], [T5]

Alex Pico

Gladstone Institutes, UCSF, USA

• Background/Skills
• Collecting pathway information into computational models
• Pathway Figure OCR, WikiPathways, and Cytoscape
• GH Actions, R Shiny apps, R/Python libs, databases, data viz
• Ideas for this hackathon
• I have the OCR content from 103,000 pathway figures published between 1995-2023, including gene, chemical, and disease names mapped to identifiers, and for hundreds of specific microbial and plant species. Let's make it more accessible and useful!
• Favorite programming language: ChatGPT 😛
• Things to share
• Co-founded WikiPathways in 2007, dedicated to open science
• I've been in Japan for the entire month of June (ask to see my photos)
• ずっと勉強していますが、まだ下手ですよ。

[R4] for [R1] + [R2], [T1], [T3], [T4], [T6]

Kozo Nishida

Tokyo University of Agriculture and Technology (TUAT), Japan

• Background/Skills
• Networks and Graphs Discovery in�Metabolomics Data Analysis and Interpretation
• MS-DIAL, WikiPathways, and Cytoscape
• R Shiny apps, R/Python libs, databases, data viz
• Ideas for this hackathon
• Automatic mapping of MS-DIAL peak intensity tables to WikiPathways and its visualization using Cytoscape.
• Favorite programming language: R and Python
• Things to share
• Dedicated to Open Science, Bioconductor Community Advisory Board, The Carpentries instructor
• Dedicated to Research Software Engineer (RSE) Asia community

[R4] for [R1] + [R2], [T1], [T3], [T4], [T6]

​

Cyril Pommier

INRAE (National Research Institute for Agriculture and Environment), France

• Background/Skills
• Plant phenotype and genetics data management
• Data formalisation, ontologies, data standards (MIAPPE, BrAPI), information systems, …
• Ideas for this hackathon
• [R4]: increase visibility of Japanese databases in the plant research data discovery portal FAIDARE
• [R4]: explore the use of the Breeding API for knowledge graph
• Favorite programming language: Java, python, bash, SQL, Elasticsearch, Neo4J/Sparql (rusty)
• Things to share
• Bridging Phenomics and Omics communities
• Biohackathons Europe and Brapi Hackathons since 2018
• Co leading data standards and ELIXIR Plant community
• Fond of Japan in general and Kendo in particular

[R4]-->[R3], [T1], [T4], [T6]

Takatomo Fujisawa

DDBJ, National Institute of Genetics, Japan

• Background/Skills
• Development and Operation of DDBJ Databases (BioProject, BioSample, DRA, GEA, JGA, MetaboBank, and JVar)
• Development of Microbial Database (MicrobeDB.jp, mdatahub.org)
• Ideas for this hackathon
• Interconversion of variant data file formats for JVar（VCF, TSV for Submission, XML for dbVar, RDF for TogoVar)
• Favorite programming language: Ruby
• Things to share
• Lost weight about 10 kg, Be on a diet, and Keep weight during this hackathon.

​

​

[R4] (will contribute to [R1], [R2]), [T1], [T4]

Kiyoko F. Aoki-Kinoshita

Glycan & Life Systems Integration Center (GaLSIC), Soka Univ., Japan

• Background/Skills
• Distributed computing, microarray analysis software
• Database and tool development
• Glycoinformatics
• Ideas for this hackathon
• Integration of glycan-related omics data with proteins, chemicals, microbes, plants, diseases, etc. into the GlyCosmos Glycoscience Portal
• e.g., MicroGlycoCurator/MicroGlycoDB
• Analysis of effects of variants on glycogenes
• Favorite programming language: Python (and Java, Ruby, C/C++...)
• Things to share
• I am responsible for developing the database infrastructure for the 10-year Human Glycome Atlas project which started this past April
• I play violin and sing in a trio called “Bonnes Amies Trio” ボナミトリオ
• I enjoy making pasta from scratch

[R4] (will contribute to [R1]&[R3]), [T1], [T5]

Núria Queralt Rosinach

Leiden University Medical Center (LUMC), The Netherlands

• Background/Skills
• Database (DisGeNET-RDF), tool (bioknowledge reviewer)
• Ideas for this hackathon
• Automatic retrieval of curated or/and text mined metabolite associations for knowledge graph construction, for example from PubChem
• Evaluate this automatic retrieval reusing it to extend an existing knowledge graph constructor tool, for example bioknowledge reviewer, or to retrieve a high quality dataset for ML/NLP
• Favorite programming language: Python
• Things to share
• I can do magics with one of my shoulders
• I am happy when I am in the water: Onsen, Ocean, Sea, Swimming pool…

​

[R4] (could contribute to [R1]), [T1], [T4], [T6]

Yoko Okabeppu

OKBP Inc., Japan

• Background/Skills
• Database engineer, Query tuning (SPARQL and SQL)
• Application Development
• Ideas for this hackathon
• I will examine data structures that represent pathways.
• I will try to tuning queries to retrieve statistics for huge ( > 50 billion triples) RDF endpoints.
• Favorite programming language: Ruby, Java, Python, JS, R, PHP
• Things to share
• Please check my nails! Don't miss it!
• I present to you Japan's three (or four) great somen noodles.

​

[R2], [T1], [T4], [T5]

Ryo Niwa

Kyoto University, Japan (PhD student: D2)

Center for iPS Cell Research and Application (CiRA)

• Background/Skills
• Microbiome analysis (16S rRNA amplicon sequencing)
• Making pipelines for conventional bioinformatics (RNA-Seq, WGS)
• I am focusing on genome editing in iPSCs as a wet researcher
• Ideas for this hackathon
• [R1] Automated and integrated gene editing design system for CRISPR-Cas9/Base editing/Prime editing with genomics
• Favorite programming language: R, bash
• Things to share
• I am a geek of ramen and udon. Very excited to visit Udon prefecture!
• Kyoto Sanga (football club) gold clue

​

[R1], [R2], [T3], [T4]

Manabu Ishii

Genome Analytics Japan Inc., Japan

• Background/Skills
• Backend, infra, cloud, engineer: �Debug, Programming, Workflow Languages, Database, Web ,,,
• Ideas for this hackathon
• Run and Create workflow a lot.
• Favorite programming language: MSX Basic, Assembler(Z80, 80x86), python, CWL, Javascript,D
• Things to share
• Beer, FC Tokyo, and soccer.�running, (Techno) Music.
• I run from Family name to�Last name, Train Stations�only 16km ! (430JPY)

[R1], [R2], [R4], [T2], [T4], [T5], [T6]

Hirotaka Suetake

Sator Inc., Japan

• Background/Skills
• Programming, Testing, UI, wf, DevOps, etc.
• Ideas for this hackathon
• No specific plan, but ready to jump in and code like a ninja.
• Favorite programming language: Typescript, Rust, Python
• Things to share
• I’m a cat lover with a cat allergy (Fig. 1, 2)

​

[R1], [T2], [T4], [T5], [T6]

Fig. 2: The allergen

Fig. 1: The victim

Rund Tawfiq

King Abdullah University of Science and Technology, Saudi Arabia

• Background/Skills
• Metagenomics
• Ideas for this hackathon
• Integrate AI tools for de novo metagenomic function prediction
• Metadata schemas for environmental data
• Favorite programming language: Python
• Things to share
• I like learning languages. Teach me a word in your language!

​

[R2], [T6]

Liisa Lado-Villar

CSC - IT Center for Science, Finland

• Background/Skills
• Terraform to build VMs as cluster, Linux, Docker, Javascript, Bash, SQL
• Ideas for this hackathon
• I would like to participate a team developing apps
• Favorite programming language: Go, this is quite new to me
• Things to share
• ​
• I like long sleeps
• Started working at CSC was happiest time
• Preparing travel to Biohackathon is the current thing

​

[R4]( [R1]), [T5], [T4], []

Ryo Nozu

Hiroshima University, Japan`

• Background/Skills
• RNA-seq data and genomic analysis
• Ideas for this hackathon
• Expansion of pathway analysis to non-model organisms. Especially, utilization of comprehensive collection of published pathway figures (collaboration with WikiPathways team)
• Favorite programming language: shell
• Things to share
• Actually,... my main research interest is reproductive biology on fish
• from tiny medaka to whale shark (the largest extant ‘fish’):D

[R3], [T1], [T3], [T6]

Kazuki Nakamae

Hiroshima University / PtBio Inc., Japan

• Background/Skills
• Genome Editing in human cells
• Amplicon DNA sequencing for genotyping
• RNA-seq for off-target analysis in genome editing
• Ideas for this hackathon
• Data mining method for RNA-seq analysis of RNA off-target induced by DNA Base Editor
• Favorite programming language: R, Python, Lua
• Things to share
• I welcome discussions on bioinformatics of genome editing at any time!
• A turtle lover 🐢…

[R1], [T1], [T3], [T4]

Takayuki Suzuki

Hiroshima University, Japan (PhD student: D1)

• Background/Skills
• RNA-seq analysis
• Knowledge extraction from PubMed/PMC (in topics with genome editing)
• Ideas for this hackathon
• Trying to study/work on the uses of LLM in knowledge extraction from literature.
• (I’ve just got my turn for the access to API key of PaLM (open source LLM by google) last week)
• Favorite programming language: Python
• Things to share
• Addicted to check NBA news and highlights

​

[R4] (will contribute to R3), [T1], [T3],[T4]

Maria Gomez

King Abdullah University of Science and Technology, Saudi Arabia

• Background/Skills
• Image and signal processing in biomedical data
• Transcriptomics, miRNA and epigenomics analysis
• Ideas for this hackathon
• Deep learning and machine learning for dimensionality reduction.
• The application of statistical methods
• Favorite programming language: Python, R, MatLab
• Things to share
• A cat lover.

[R1] , [T3],[T5]

Gos Micklem

University of Cambridge, United Kingdom

• Background/Skills
• InterMine project lead; molecular biologist turned computational biologist
• Ideas for this hackathon
• reverse-engineering data model from RDF (using sheXer + LLM??)
• pan-model organism database querying
• Favorite programming language:
• Ostensibly {Python, Lisp} but actually English and Perl
• https://www.explainxkcd.com/wiki/index.php/224:_Lisp
• Things to share
• Probably will be on sabbatical at DBCLS October 2023 - April 2024!
• Have not tasted 600 sakes yet but...
• Got to diamond league in Duolingo Japanese (by gaming the system)

​

[R1], [T1], [T3], [T4]

Masaki Fukui

Sator Inc., Japan

• Background/Skills
• Backend engineer Tool development, programming,
• Ideas for this hackathon
• No specific plans, but eager to learn about workflow and making tools.
• Favorite programming language: Rust, Python
• Things to share
• I listen to metal music a lot.
• Going to attend a Cynic concert in December, which they are holding in Japan for the first time since 2015.

​

[R4], [T2], [T4],[T5]

Taro Kakuzaki

Sator Inc., Japan

• Background/Skills
• Bioinformatics, Machine Learning, protein-LLM
• Ideas for this hackathon
• I don't have a concrete idea, but I would like to be able to utilize LLM to RDF data.
• Favorite programming language: Python, R
• Things to share
• I used to climb mountains in Japan. Please feel free to ask me as I know some recommended mountains in Japan.

[R2], [T2], [T3],[T4]

Tatsuya Kushida

RIKEN BioResource Research Center (BRC), Japan

• Background/Skills
• Database integration, RIKEN Bioresource knowledge graph
• Ideas for this hackathon
• Extension of the bioresource KG to enhance information and knowledge of the RIKEN bioresources
• Development of ID mapping data derived from the KG (e.g., relationships between bioresource IDs and the related Gene IDs, UniProt AC, PubChem CIDs, GO terms, disease ontology ID & label)
• Interested in: A DBCLS product TogoID system to make the mapping data.
• Favorite programming language: SPARQL
• Things to share
• Rugby World Cup FRANCE 2023 (8 Sept. - 28 Oct.)

​

[R4] ([R1], [R3]), [T1], [T5]

Hiroshi Masuya

RIKEN BioResource Research Center (BRC), Japan

• Background/Skills
• Integrated Database, BioResource KG
• Ontology
• BioResources: Mouse, Plant, Culturing Cell, Microbe, Genetic clone
• Mouse developmental genetics
• Ideas for this hackathon
• Disease model exploring based on phenotypic equivalence
• Association of genomic elements (CREs) with phenotypes/diseases
• Favorite programming language: SPARQL
• Things to share
• Attending: June 25 (Sun) to 27 (Tue), leaving 28 (Wed)

​

[R (1, 2), 3, 4], [T1]

Hiromi Kajiya-Kanegae

Research Center for Agricultural Information Technology, NARO, Japan

• Background/Skills
• Plant Breeding, Bioinformatics
• Pedigree Finder: A Web-based Viewer for Knowledge Graphs of Crop Pedigrees.
• Genomic selection for crop improvement.
• Ideas for this hackathon
• [R3]Data-driven interdisciplinary studies in agriculture and other fields.
• Favorite programming language: R
• Things to share
• I have a sweet tooth.

​

[R3], [T1], [T4]

Tomoya Tanjo

National Institute of Genetics, Japan

• Background/Skills
• Workflow languages, Workflow engines (esp. CWL)
• Ideas for this hackathon
• Develop workflow-related tools
• Help you to develop your workflows
• Favorite programming language: Common Workflow Language, D
• Things to share
• Let’s write your workflows in CWL!
• See also: Starting CWL with `Zatsu` method!

​

[R2], [T2], [T4], [T6]

Issaku Yamada

The Noguchi Institute, Japan

• Background/Skills
• Organic chemistry, Glycoscience
• Database and tools for glycoscience
• Structure representation (InChI/InChIKey, SMILES, WURCS, GlycoCT and …)
• Ideas for this hackathon
• Integration of glycan-related omics data.
• Favorite programming language: C#, Java? PHP? Python?
• Things to share
• What is monosaccharide?
• Recruiting Lab. members.
• For the first time in my life,

​

[R4] (will contribute to [R1]&[R3]), [T1], [T4], [T5]

• This rabbit was designed by me.　⇒

I was told I wasn't tone deaf.

Atsuko Yamaguchi

Tokyo City University, Japan

• Background/Skills
• Database, Graph algorithms, Tool development
• Umaka suite, Algorithms for PubCaseFinder, RDFization of the disordered protein database, etc.
• Ideas for this hackathon
• Maybe [R3]
• Favorite programming language: Java, C++, SPARQL, Python
• Things to share
• I moved to Tokyo City University from DBCLS in 2020 and am teaching data science classes.
• I love creating fabric accessories with my child.

​

[R3], [T1], [T2], [T5]

François Belleau

Arnaud Droit Computational Laboratory, Canada

• Background/Skills
• Bio2RDF architect and Linked Data specialist
• BH2017 Semantic web evangelist
• System and Elasticsearch administrator at ADLab a multi-omics research laboratory hosting Kibio.science
• Ideas for this hackathon
• [R4] Teach a popular open-source BI tool, Superset, some SPARQL to help visualize Semantic Web resources, thereby democratizing the knowledge graph of Linked Data in the life sciences.
• Favorite programming language: SPARQL, Python, SQL
• Things to share
• Captain of an Alberg 37 feet sailboat
• Available to collaborate for semantic and FAIR projects

​

[R4] for R1, [T1, T4, T5]

Orion Buske

On sabbatical from PhenoTips, Canada

• Background/Skills
• Computer science, genomics → Leading startup for last 5 years
• Patient matchmaking, Human Phenotype Ontology, GA4GH pedigree standard
• Rare Disease Doctors (BH19), VariantFacts (BH17), PhenomeCentral (MME)
• Ideas for this hackathon

Evaluate LLMs (e.g. GPT4) for genomic medicine:

• Rare disease diagnosis, esp. patient matchmaking and CDS
• Terminology translation/concept recognition (especially HPO)
• Patient intake (consent, family history)
• Favorite programming language: Python, bash, javascript
• Things to share
• Just co-organized diagnostic hackathon in Sweden last week
• Loves back-country canoe camping and foraging (gourmet) mushrooms

[R4] (will contribute to [R1]), [T1], [T2], [T4]

Susumu Goto

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Previously developed KEGG databases, especially enzyme reactions.
• Currently not so much in development, but involved in proteomics database, bioresource database integration, etc.
• Ideas for this hackathon
• Interested in data integration and method developments for predicting growth media of newly sequenced bacteria.
• Favorite programming language: Perl
• Things to share
• Likes: walking, singing, playing and watching baseball, but not doing so much in these two month for my back pain

​

[R2], [T1], [T2], [T3]

Nobutaka Mitsuhashi

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Integration of human genetic variations (TogoVar)
• Ideas for this hackathon
• I can provide human genetic variant data in various formats.
• I would like to integrate anything with the variants in TogoVar to help interpretation of human genetic variations.
• e.g. structural variants, counterpart mouse variants and eQTL data.
• Favorite programming language: Python, CWL (now learning)
• Things to share
• Only ten minutes of jogging or walking in the morning refreshes and energizes me for work.

​

[R1], [T1], [T5]

Daisuke Satoh

Kamonohashi Inc., Japan

• Background/Skills
• Web app backends
• TogoVar
• TogoDX
• YummyData (UmakaData)
• Tools
• Namahage (VCF validator)
• Ideas for this hackathon
• No specific plans, but I can help with prototyping, making applications, tools, etc…
• Favorite programming language: Ruby, Rust
• Things to share
• In the middle of Shikoku 88 temple pilgrimage (by bicycle)
• Finished until 59th temple last year
• Plan to restart from 60th temple after this hackathon

[R1], [T4], [T5]

• Background/Skills
• Bioinformatics, Ontologies, Data integration, Personalized health
• LinkML, Biolink Model, Knowledge Graph Hub, SPHN
• Ideas for this hackathon
• Implementation of a redesigned LinkML Validator
• Open to work on other exciting topics!
• Favorite programming language: Python
• Things to share
• This will be my third BioHackathon :D
• Currently hopping countries
• USA (2012)
• Germany (2021)
• Switzerland (2022)
• Curious about peaty/smoky whiskies

Deepak Unni

SIB Swiss Institute of Bioinformatics, Basel, Switzerland

[R1], [R4], [T1], [T4], [T5]

Yasunori Yamamoto

​

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• RDF, Text Processing
• Allie, Umaka-YummyData, rdf-doctor, etc.
• Ideas for this hackathon
• Anything related to LLM, RDF, OWL, ShEx.�Current interest is to refine RDF data by using sheXer,�OWL reasoning.
• Favorite programming language: Perl, Python, Java, SPARQL
• Things to share
• Walking with a dog.
• Long walking along Sumida river (>10km).
• Seeing maps.
• My PC has been broken.

[R3], [R4], [T1], [T4], [T5]

Naoshi Koide

Osaka University, Japan

• Background/Skills
• Cell biology
• Regenerative medicine(iPS Cell derived retina)
• Humanities
• Liberal arts
• Ideas for this hackathon
• Bridging between pure science and social issues
• Liberal arts design across disciplines and specialties
• Favorite programming language: xxx
• Things to share
• This is my first (bio)hackathon!

​

[R4] (will contribute to [R3]), [T5]

Akihiro Fujita

Soka Univ ,Glycan & Life Systems Integration Center (GaLSIC), Japan

• Background/Skills
• Glycoinformatics
• Database and tool development
• Ideas for this hackathon
• The development of GlyTouCan is the glycan repository
• Organizing Glycan Data Using Ambiguous Structures (Glycan Subsumption)
• JRuby Wrapper library for tools for glycoinfomatics written in Java
• Favorite programming language: Ruby(JRuby)
• Things to share
• I’m arriving here via an overnight train
• I started paying for chatgpt plus today
• I just noticed additional cost to use api (T_T)

[R1], [T1], [T5]

Andrea Ghelfi

National Institute of Genetics, Japan

• Background/Skills
• Developed pipeline for a file check and fix for annotation and fasta files submitted to DDBJ to allow faster curation
• Ideas for this hackathon
• Develop a database/app for monkeypox metadata using SurrealDB/Rshiny
• Challenge: implement authentication system for private data
• Favorite programming language: R
• Things to share
• I like to play Blues on bass guitar
• I am really glad to join this BH

​

[R4],[R3], [T1], [T5]

Mari T. Minowa

Database Center for LifeScience(DBCLS), Japan

• Background/Skills
• Molecular Biology
• NBDC human database
• Public Relations
• Ideas for this hackathon
• A member of help desk
• Favorite programming language: ???
• Things to share
• I would like to help everyone enjoy their time on Shodoshima.
• Recently, I have been growing vegetables in my garden, such as petit tomatoes, cucumbers, eggplants, okras…

​

[R1], [T1]

Soichi Ogishima

ToMMo, Tohoku University, Japan

• Background/Skills
• Data integration of genome cohort and biobank
• Deep phenotyping and risk prediction of common diseases (low-birth-weight and hypertensive disorders of pregnancy)
• Ideas for this hackathon
• Explore hypotheses explaining molecular mechanisms causing disease phenotypes by important genomic and exposure factors
• Discuss a future framework that enables real-time �feedback through RWD research in the coming genomic �society
• Favorite programming language: Perl, R, Python
• Things to share
• Have a drink at Mamemame microbrewery!

​

[R1], [T1], [T4]

Moses Njagi Mwaniki

UniPi, University of Pisa, Italy

• Background/Skills
• Algorithms for genome graphs
• Tool development
• Ideas for this hackathon
• [R1] To allow for fast queries with regards to variants in genome graphs, decompose the variable regions of a genome/variation graph into a tree structure
• Favorite programming language: Rust, C++
• Things to share
• I have been trying to learn Italian
• I want to learn more about Japan :-D

​

[R1] [T1] [T2] [T5]

Yuichi Shiraishi

National Cancer Center Research Institute, Japan

• Background/Skills
• Managing cancer genome analysis pipeline (Genomon).
• Software for detecting somatic SVs in cancer genome using long-read (nanomonsv).
• Infrastructure for pathogenic variant detection using public sequence repository (SAVNet, IRAVNet).
• Developing statistical methods based on probabilistic models.
• Ideas for this hackathon
• Tools for developing cancer genome structure graph.
• Favorite programming language: python, R
• Things to share
• Mountain hiking, running, walking around.

[R1], [R4], [T1], [T2]

Thomas Liener

Austria

• Background/Skills
• FAIR data, Semantic Web, Data integration
• Ideas for this hackathon
• Multilinguality (of ontologies)
• Favorite programming language: Python
• Things to share
• If travelling, I like diving (for example with sharks) �and hike (for example to active volcanoes) :)
• I like snowboarding in winter

​

[R1], [T2], [T3]

Mayumi Kamada

Kyoto University, Japan

Center for digital transformation of healthcare

• Background/Skills
• Development of databases for genomic medicine
• Development of machine learning models and three-dimensional structural analysis to predict the disease relevance of genomic variants
• Ideas for this hackathon
• Integration and utilization of multimodal data in machine learning
• Favorite programming language: Python（,Ruby）
• Things to share
• I love Beer, Ramen, Highball(whisky and soda)
• I enjoy changing up my look at the hair salon 💇‍♀️

​

[R1],[R4], [T1],[T3], [T5]

Masaaki Matsubara

The Noguchi Institute, Japan

• Background/Skills
• Glycoinformatics, Cheminfomatics
• Glycan structure representations (WURCS, GlycoCT, …)
• Ideas for this hackathon
• Integration of glycan-related omics data
• Glycan data integration with PubChem using WURCS
• Favorite programming language: Java(, PHP, Perl)
• Things to share
• Main developer of WURCS (Web3 Unique Representation of Carbohydrate Structures)
• I was born in Kagawa

[R4] (will contribute to [R1]&[R3]), [T1], [T4], [T5]

Erik Garrison

University of Tennessee Health Science Center, Memphis, TN, USA

• Basic bioinformatic methods / pangenome graphs
• Ideas for this hackathon
• Will be working on a new way to call variants from pangenome graphs.
• Favorite programming language: rust
• Things to share
• I make strange livecoding electronic music
• Working on DNA synthesis and DNA computing!
• Live in both west tennessee and south italy
• Like running when it’s really warm or really cold
• Recently: impromptu volunteer firefighter→

​

[R1], [R2], [R4], [T1], [T2], [T4]

Jaemoon Shin

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Database, tool development (PubCaseFinder-RDF, PanelSearch)
• Ideas for this hackathon
• Constructing virtual gene panel and adding variant data using RDF
• Favorite programming language: java
• Things to share
• I like spicy food.

​

[R1], [T1], [T5]

Keiko Sakuma

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Research support staff
• Ideas for this hackathon
• Hope the BH23 goes well. I would be willing to support you as a help desk for this purpose.
• Favorite programming language: ー
• Things to share
• My hobby is 🎾🧘🍵⛩️.
• Shodoshima Island is famous for Somen noodle, and my hometown(Shimabara, Nagasaki) is too. In BH23,I would like�to compare various somen noodles!

​

Satoshi Onoda

Yohak LLC, Japan

• Background/Skills
• Frontend engineer / Designer / NO ACADEMIC BACKGROUND
• Ideas for this hackathon
• Getting real user voices for improving togomedium.org
• Possibly contributing other projects from the visual/UX standpoint.
• Favorite programming language:
• TypeScript / HTML / CSS
• Things to share
• (Before marriage) I used to be a backpacker, traveled around the world, enjoyed talking and drinking with locals.

[R2], [T1], [T4], [T5]

Yoshitaka Sakamoto

National Cancer Center Research Institute, Japan

• Background/Skills
• Cancer genome analyses using long-read sequencing data
• Ideas for this hackathon
• Develop a cancer genome analysis pipeline
• Favorite programming language: Python
• Things to share
• Like swimming and seeing NBA results
• Started my PhD career in April this year

​

[R1], [T1], [T3]

Andra Waagmeester

Micelio, Belgium

• Background/Skills
• Background in Biomedical Informatics, keywords: �FAIR, Linked Data, Wikidata/Wikibase, Wikipathways RDF, �Shape Expressions
• Ideas for this hackathon
• Identifying and describing subsetting patterns in large RDF graphs using Shape Expressions
• Aligning Pathways RDF representations
• Favorite programming language: Bash, Python, ShEx, SPARQL
• Things to share
• Next to a professional life working with RDF, I like to observe nature and mint URIs for every observation
• I brought with me a LepiLED.
• I organise BioHackathon SWAT4HCLS

​

[R4 (R2-R3], [T1], [T3]

Eric Prud’hommeaux

Clermont-Ferrand, France

• Background/Skills
• Mechanical engineering
• (Sem)Web standards
• Ideas for this hackathon
• Introducing a SPARQL endpoint to the HAPI FHIR library for use in research
• Favorite programming language: C++, Typescript, ShEx
• Things to share
• I like inventing languages
• Want to merge clinical research and personal medicine

​

[R4 (R1,R3], [T1], [T5]

Claude Nanjo

San Diego, CA (Medontology, University of Utah)

• Background/Skills
• Clinical Data Modeling & Knowledge Representation
• Clinical Decision Support
• Shape Expressions
• Health Interoperability Standards at HL7
• Ideas for this hackathon
• Introducing a SPARQL endpoint to the HAPI FHIR library for use in research
• Favorite programming language: Java, ShEx
• Things to share
• Trying to grow cherry trees in California
• Going to Africa
• Improving care through better EHRs

​

[R4 (R1,R3], [T1], [T5]

Yosuke Kawai (河合洋介)

National Center for Global Health and Medicine(NCGM), Japan

• Background/Skills
• Population Genetics and Molecular Evolution(mainly human)
• Medical Genetics (rare disease)
• Ideas for this hackathon
• Starandarize human genetic variation for MGeND
• Create ancient human genome database
• Favorite programming language: Python, MSX BASIC
• Things to share
• First time attending BH

​

[R1], [T1], [T3], [T5]

Eisuke Dohi

National Center of Neurology and Psychiatry (NCNP),

National Institute of Neuroscience, Tokyo, Japan

• Background/Skills
• Physician (rare diseases), Neurologist 10y
• Neuroscience(mouse behavior), molecular biology(Extracellular Vesicles)
• Collaboration: PubCaseFinder, data extraction from rare disease pts, Japanese translation of MPO
• Ideas for this hackathon
• LLM projects for patient data.
• The issues between MPO and HPO?
• Interpretation of human genetic mutation, etc
• Favorite programming language: python???
• Things to share
• Undiagnosed Hackathon(Orion. 5/16-18, Sweden)
• I started learning to draw (last Thursday)

[R4] (could contribute [R3]), [T3], [T5], [T6]

Kentaro Yamamoto

Genome Analytics Japan Inc., Japan

• Background/Skills
• RIKEN（2019-2023 March, Nikaido Lab）-> GAJ（April〜）
• WormTensor：R&Snakemake（article published last week）
• Everyday run workflow a lot ,with GAJ Members Hachiya(Boss) and ishii
• Ideas for this hackathon
• I will examine how to make R Package
• (Sorry,Tensor Decompositon a little ……)
• Favorite programming language: R, snakemake　(learning CWL)
• Things to share
• Unfortunately, My Team（FC Tokyo） rank down 11/18
• But, tomorrow won（2-0）!!
• I am novelist（not famous）.

[R1], [T2], [T3]

CRAN

Package

Article （bioinfomatics）

Article

（science fiction）

lost again

today‥

coworker

and FC東京 supporter

Twitter🐦：@yamaken37

Masashi Yokochi

Protein Data Bank Japan (PDBj)

• Background/Skills
• NMR (nuclear magnetic resonance)
• Developer/maintainer of wwPDB/RDF, BMRB/RDF
• Ideas for this hackathon
• Translate PDB/BMRB’s jargons to biohackers
• Favorite programming language: Python, Java
• Things to share
• Happy to know Alpha-fold, except for my job

​

[R1], [R2], [T1]

Toyofumi Fujiwara

Database Center for Life Science (DBCLS), Japan

• Background/Skills
• Engineering and biomedical data
• PubCaseFinder (short intro) and NANDO
• Ideas for this hackathon
• AI-based phenomics to support clinicians in diagnosing patients
• Favorite programming language: Perl, Python
• Things to share
• We are looking for colleagues to work with us at DBCLS!
• https://ds.rois.ac.jp/saiyou/2023/post-8641/
• The deadline for applications is June 30.

[R3], [T1], [T5]

Robert Hoehndorf

King Abdullah University of Science and Technology, Saudi Arabia

• Background/Skills
• Computer scientist and logician, focusing on Semantic Web
• Combining logic and learning (knowledge-enhanced learning)
• Ideas for this hackathon
• Data model, data and tool for annotation of variants in pangenomes
• Knowledge graphs for annotating microbes, protein function prediction
• Favorite programming language: Groovy, (Coq)
• Things to share
• Big fan of Onsen

[R4], [T1], [T4]

Arriving later

Akio Nagano (PENQE)

Anton Zhuravlev (PENQE)

Yui Asano (Swallow Design Studio)

Shin Kawano (Kitasato U)

​

​

Anton Zhuravlev

PENQE Inc., Japan

• Background/Skills
• Frontend (D3.js, React, Svelte, …), UI, backend (Node), python
• Ideas for this hackathon
• Helping people to visualise their data (?)
• Favorite programming language:
• TypeScript/JavaScript
• Things to share
• I draw
• Trying to do standup comedy
• Snowboarding

[R4], [T1], [T4], [T5]

Akio NAGANO

PENQE Inc., Japan

• Background/Skills
• Graphic design, Illustration, Front-end engineering
• I am involved in the following projects
• TogoDX
• TogoVar
• RefEx
• REBIND
• Ideas for this hackathon
• I give shape to your ideas.
• Favorite programming language: MZ BASIC, MSX BASIC, LINGO, ActionScript, Objective-C, JS, TS
• Things to share
• Collect stickers
• Collect word histories

​

[T5] Application

Yui Asano

Swallow Design Studio, Japan

• Background/Skills
• I created this hackathon design 2023.
• UI design for PubCaseFinder and PanelSearch
• CaseSharing:beta development
• Ideas for this hackathon
• I am looking for what I can do.
• Favorite programming language: ???
• Things to share
• I like bird watching.
• My favorite bird is Great tit.

[]

I made poster 2018.

This seagull was taken in Stockholm.

Shin Kawano

Kitasato University, Japan

• Background/Skills
• Proteomics
• jPOST
• Ideas for this hackathon
• Efficient representation of meta-proteome data
• collaboration with RefEx for proteomics data
• metadata extraction from literatures
• Favorite programming language: Ruby
• Things to share
• I moved Kitasato Univ. from this April.
• I like junmai sake.

​

[R1], [R2], [T1], [T3]