DBCLS BioHackathon 2010

The 3rd DBCLS BioHackathon for interpreting biological knowledge with Semantic Web technologies will be held during 2010/2/ 8-12 in Japan.


DBCLS is working on the integration of biological resources. To achieve this goal, we have been organizing BioHackathons since 2008 to survey existing efforts and develop integrated environments with open source software and public services. Themes of the hackathons evolved year by year, and we are continuously providing cutting edge developers with opportunities to gather for utilizing state of the art technologies to emerging demands in life sciences.

  • 2008 : Towards interoperable web services in life science with Open Bio* libraries
  • 2009 : Integration of web services in bioinformatics applications
  • 2010 : Interpretation of biological knowledge with the Semantic Web technologies

Facing to unprecedented amount and variety of biomedical data, it is required to consolidate related information and facilitate efficient interpretation of the accumulated biological knowledge. Therefore, we selected the Semantic Web as its main theme this year. Topics may include but not limited to:

  • Queries
    • Targeted queries to be resolved by the Semantic Web technologies.
  • Datasets
    • List currently available and/or still missing datasets (as Linked Data / RDF) to resolve the above queries.
  • Stores
    • Develop our own or survey existing extensible storage systems for RDF triples and functional query interfaces.
  • Tools
    • Develop common APIs among Open Bio* projects for RDF stores and SPARQL endpoints.
    • Develop a set of programs including loaders and converters for RDF data.
    • Develop supporting text mining systems and end-user applications.

About the Hackathon

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

BioHackathon 2010 is sponsored by Database Center for Life Science ( DBCLS) and Computational Biology Research Center ( CBRC). DBCLS is a national center responsible for sustainable life science databases in Japan and CBRC is a national research organization for bioinformatics.

Domestic announcements

バイオハッカソン 2010 は日本国内からの参加者を募集中です。 予算の都合により今年度の国内参加者は招待制ではありませんが、今回の開催趣旨に賛同頂ける研究者・開発者の方々の積極的なご参加をお願い致します。 また、世界トップレベルの開発者と最先端の課題についてディスカッションできる絶好の機会ですので、将来を担う若手研究者・学生の参加枠も設ける予定です。


2010/2/8 @  CBRC (Odaiba, Tokyo)

  • for the 1st day (Symposium and banquet)

2010/2/9-12 @  DBCLS (Nezu, Tokyo)

  • rest of the days (hack, hack, hack)


Access -- see also the "Transportation in Tokyo" section below

  • From  Tokyo Narita International Airport
    • Narita airport station -> Keisei Ueno station (75 min, 1000 JPY by Keisei line; 60 min, 1920 JPY by Keisei Skyliner)
    • Take a taxi from Ueno station to your hotel (or to DBCLS)
  • From  Tokyo Haneda Airport -- for the group from Korea
    • Haneda airport station -> Hamamatsucho station (20 min, 470 JPY by Tokyo monorail line)
    • Hamamatsucho station -> Ueno station (10 min, 160 JPY by JR line)
    • Take a taxi to the Sanjokaikan faculty house in University of Tokyo

Annotated Google Maps and KML file for Google Earth are available:


Mailing list

Live streaming

Official hash tag

  • #biohackathon2010 -- official hash tag for  twitter, citeulike and so on.

Social networks


SVN repository


How to obtain your account to edit this wiki site?

  • Your account for the wiki will be issued on request. Please send an e-mail containing desired login name and encrypted password to mn@… (Mitsuteru Nakao).
  • You can use 'htpasswd' command to generate encrypted password (htpasswd -n LOGIN_NAME).

You are encouraged to bring/prepare:

  • Laptop computer and conversion plug for your AC adaptor (identical to the US type; 100 volt, Type-A shape  Wikipedia)
  • Some local liquor as always (for the banquet and the Liquorthon at night, as alcohol drinks can't be provided by our budget :-)
  •  LinkedIn account to share your profile with others (please link by yourself at Participants)

Transportation in Tokyo

Dining & drinking

  • recommend a nice bar: Orange
    •  MidTown 1st floor Orange PS: Green Arrow showes location. Sorry, the map is in Japanese. Address in English : Tokyo, Minato-KU, Akasaka 9-7-1, Midtwon East 1F

Get Oriented

  • DBCLS is located at the "Yanesen" area, where there remains a traditional Japanese atmosphere. Check  this article out!