Version 16 (modified by ktym, 15 years ago)


BioHackathon 2009

Integration for the wet biologists - bring the cutting edge technologies to the bench.


The hackathon (hacking + marathon) basically is a camp where invited participants discuss about current issues and implement software to solve the problems on site collaboratively. This kind of meeting is very effective for the intensive development of projects because face-to-face meeting of developers, who usually spread around the world, accelerates communication and collaboration to exchange their ideas instantly.

In addition to gather database and service developers, we will also involve semi-wet biologists working in a area where high throughput gene annotation is required because they are primary consumers of our infrastructure. By knowing their demands, we can find what kind of resources are missing and prioritize our action items.


Main objective of the meeting is to continue global efforts to standardize biological database resources and to improve usability and interoperability of bioinformatics services, which were proposed in the previous meeting.

The agenda of the previous meeting, BioHackathon 2008, is available at

Additionally, we will collaborate with

  • Organizations which have similar mission with us (e.g. ELIXIR) for the complemental efforts.
  • Developers of integrated platforms like BioMart, GMOD, Galaxy etc.

to make our previous efforts to be utilized by the scientific researchers effectively.


Technology: Infrastructure and standardization

  • Integration of the integrated databases - Unified API for distributed services
  • Agreement on common exchange data formats, ontologies and semantics
  • Provide stable and interoperable services with SOAP and REST
  • Manifesto and guidelines for the next generation

Application: Mash-up and user friendly interface

  • Improve end-user applications like Galaxy to utilize integrated databases and services
  • What kind of databases and services are currently missing for the real science?
    • e.g. Genome-scale analysis: pipelines and visualization

Promotion: Outreach to the wet biologist

  • Hands-on seminar
  • Documentation


  • Improve Open Bio* libraries and other tools to apply real world issues.
  • Discuss about the guidelines (manifesto) towards standardization of data types and protocols for the integration of databases and services.
  • Publicaition of a meeting report.

Mailing list

Sponsor and organizers

This meeting is co-hosted by  DBCLS and  OIST, and flights and accommodation fees will be covered by their budget.

  • Toshiaki Katayama (TogoDB, TogoWS, KEGG API, BioRuby?; HGC, Japan)
  • Shuichi Kawashima (KEGG API; HGC, Japan)
  • Takeshi Kawashima (Marine genomics; OIST, Japan)
  • Mitsuteru Nakao (TogoWS, BioRuby?; Kazusa DNA Res, Japan)
  • Yasunori Yamamoto (DBCLS, Japan)
  • Atsuko Yamaguchi (DBCLS, Japan)
  • Toshihisa Takagi (Head of DBCLS, Japan)

Confirmed participants

  • Alberto Labarga (Dasty3, Elsevier Grand Challenge, EBI;, Spain)
  • Arek Kasprzyk (BioMart; OICR, Canada)
  • Oswaldo Trelles (MOWserv; Universidad de Málaga, Spain)
  • Jan Christian Bryne (EMBRACE, ELIXIR; Bergen Center for Computational Science, Norway)
  • Kiyoko Kinoshita (RINGS; Soka Univ, Japan)
  • Hideaki Sugawara (WABI/SABI; DDBJ, Japan)
  • Naohisa Goto (BioRuby?; Osaka Univ, Japan)
  • Kazuharu Arakawa (G-language; Keio Univ, Japan)
  • Keiichiro Ono (Cytoscape; UCSD, U.S.)



  • 2009/3/22-28 (to be confirmed)


  • Tokyo (DBCLS) - for the 1st day (reception and symposium)
  • Okinawa (OIST) - rest of the days (hack, hack, hack)

Our preliminary plan is to gather on Sunday in Tokyo for the reception (and symposium?), then fly together to Okinawa on Monday and back to Tokyo on Saturday after we tired of the hacking activities.

Call for signature campaign (aka Yes We Can!)

The venue, OIST, is headed by Dr. Sydney Brenner and if our hackathon can get 'go sign' by him, we'll be able to utilize more facilities at OIST (including conference halls, guest houses and meals!) which will make the quality of our meeting better. Otherwise, we need to book them in a nearby hotel, which means we need extra costs and resulted in decreasing the number of participants to be invited.







  • Arek Kasprzyk for "Database"
  • Alfonso Valencia for "Bioinformatics"
  • Alex Bateman for "NAR"


3/22 (Sun)

3/23 (Mon)



  • 基調講演 1〜4 本 (30〜60min)
  • ショートトラック 1〜6本 (10min)




  • JAL: HND 14:40 - 17:30 OKA
  • ANA: HND 15:30 - 18:15 OKA


3/24 - 3/27

Time 3/24 (Tue) 3/25 (Wed) 3/26 (Thu) 3/27 (Fri)
8:00 breakfast breakfast breakfast breakfast
9:00 hack, hack, hack hack, hack, hack hack, hack, hack hack, hack, hack
12:00 lunch lunch lunch lunch
13:00 hack, hack, hack hack, hack, hack excursion summarize
17:00 progress report progress report progress report overall presentation
18:00 dinner dinner dinner dinner
20::00 hack, hack, hack hack, hack, hack hack, hack, hack closing remarks

3/28 (Sat)

  • 那覇にて解散
  • スタッフは後片付け。ダイビングとか。


What you should bring with you?

  • Laptop computer
  • Conversion plug for your AC adaptor (identical to the US type; 100 volt)

Photo Album




SVN repository



  • とりあえず議事録をメモしておいて、この Trac を近日中に英語化する。
  • この Trac のロゴを hackathon 用に変える
  • BioHackathon? 2008 のミーティングレポートのドラフト(今週末) -> 片山, 荒川, (中尾?)
  • Hackathon 用の Twitter を作る
  • 日程調整を終わらせる
    • 2009/03/22 (Sun) -2009/03/28 (Sat) が今のところ最有力(まだ確定ではない)
    • 農芸化学会と重なる
    • 事務方が3月最終週で問題ないかを確認
  • 残りの参加者を調整する
  • エディターとのコミュニケート
  • 顔写真を集める - 名刺をあらかじめ作っておく
  • ミッションを説明するスライドを準備しておく(初日に 30 分くらい喋る)
  • TogoWS を web server issue に問い合わせる