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.

• Participants
• Schedule
• Symposium
• Hackathon
• MeetingReport

About the Hackathon

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 are usually spread around the world, accelerates communication and collaboration to exchange their ideas. BioHackathon 2010 is sponsored by the Database Center for Life Science ( DBCLS) and Computational Biology Research Center ( CBRC), and will be held in Tokyo, Japan.

• DBCLS Biohackathon 2010 http://hackathon3.dbcls.jp/
• DBCLS Biohackathon 2009  http://hackathon2.dbcls.jp/
• DBCLS Biohackathon 2008  http://hackathon.dbcls.jp/
• DBCLS  http://dbcls.rois.ac.jp/en/

The DBCLS is being accepted as a national center for the sustainable life science databases in Japan.

Objectives

• To realize semantic search framework
• To establish High-performance storage system for semantic data
• To federate Linked Data
• To use, reuse, mashup and mix the biological data on Semantic Web

Pre-hackathon discussions

• Queries
  • Example queries to be resolved by Semantic Web technologies
• Datasets
  • Bio2RDF
  • Linked Data
  • What kind of data are currently missing (as RDF) to resolve the above queries?
• Tools
  • Open Bio* -- "creating generic-yet-usable end user tools that work directly with the RDF graph data model"
• Stores
  •  Virtuoso  4store AllegroGraph?  Sesame  Jena  Redland  Mulgara  bigdata
  • RDB, Key-value store?
• Interfaces?
  • SPARQL
  • InterMine
  • Galaxy
  • BioMart
  • Cysoscape

• how to re-organize existing databases
• how to semantically annotate data (id, link, ontology)
• how to store and search triples
• how to utilize triples in open bio*
• how to query biological questions and get results
• how to scale for large amount of data
• how to utilize via web services
• how to visualize (what kind of user interface is required)

Mailing list

•  http://kml.dbcls.jp/pipermail/biohack3/
• biohack3_at_kml.dbcls.jp

Venue

• Odaiba, Tokyo (CBRC) - for the 1st day (Symposium and Reception)
• Nezu, Tokyo (DBCLS) - rest of the days (hack, hack, hack)

Access

•  CBRC (Odaiba, Tokyo venue)
•  DBCLS (Nezu, Tokyo venue)

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

•  Google Maps for the BioHackathon 2009
•  KML file for Google Earth

Housing

Misc

What should you bring with you?

• Laptop computer
• Conversion plug for your AC adaptor (identical to the US type; 100 volt)
• Local liquor as always (for the Liquorthon at night or for the reception :-)
•  LinkedIn account to share your contact address

SVN repository

• http://hackathon3.dbcls.jp/svn/

Playgrounds

• MediaWiki?  http://beta.dbcls.jp/wiki
• OpenRDF Sesame2
  •  http://beta.dbcls.jp/openrdf-sesame
  •  http://beta.dbcls.jp/openrdf-workbench

Streaming and social networking

•  http://www.ustream.tv/channel/biohackathon2010
• IRC:

•  http://friendfeed.com/rooms/biohackathon-2010 -- FriendFeed room for BioHackathon 2010
• #biohackathon2010 -- official hash tag for  twitter, citeulike and so on.
•  LinkedIn Group

Photo album