BioHackathon 2009

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

Hackathon

This hackathon 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 efficient for the intensive development of projects which involve developers usually spread around the world. Face-to-face discussion accelerates their communication and exchange of ideas with top-level developers will bring effective result.

Objectives

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

 http://hackathon.dbcls.jp/

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.

Topics

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 (e.g. TogoDB) and services (e.g. TogoWS)
• 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, learn from the world

• Hands-on seminar
• Documentation, TogoTV

Goals

• 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

•  http://kml.dbcls.jp/pipermail/biohack2/
• biohack2@…

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; scientifik.info, 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.)

Venue

Date

• 2009/3/22-28 (to be confirmed)

Place

• 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.

Housing

TO BE CONFIRMED

Access

TO BE DESCRIBED

Publication

TO BE DISCUSSED

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

TODO

• 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
  •  http://g2.trac.bx.psu.edu/wiki/GalaxyTeam
• 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

Schedule

3/22 (日)

• 成田着、ホテルや DBCLS まで各自移動
  • 成田国際線到着全便一覧  http://www.narita-airport.or.jp/ais/flightall/inter_arr.html
  • 朝か夕方が多そう
• 17:00-21:00 DBCLS にて適宜レセプション
• 外国人は都心のホテルに収容

3/23 (月)

公開シンポジウムを開催するかどうか高木先生と相談

9:00-12:00

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

会場は東京駅か品川駅近辺

• 東京ステーションカンファレンスセンター（サピアタワー）  http://www.tstc.jp/access/
• 東京コンファレンスセンター・品川  http://www.tokyo-cc.co.jp/access.html

お昼ご飯は会場でケータリングかお弁当

羽田までは空港リムジンバスを事前予約しておく（チャーターより割安）

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

着いてから那覇で食事？バスをチャーターして会場兼ホテルに移動

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 (土)

• 那覇にて解散
• スタッフは後片付け。ダイビングとか。

Misc

What you should bring with you?

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

Photo Album

IN PREPARATION

Streaming

IN PREPARATION

SVN repository

IN PREPARATION