Version 53 (modified by ktym, 13 years ago)


BioHackathon 2008

Towards integrated web service in life science with Open Bio* libraries.


The number of web service providers in bioinformatics field is increasing year by year. In theory, these services are interoperable and independent from computer languages. However, each service uses their own definition of the data types and naming conventions for the methods. Moreover, these services are often not usable by specific languages (partly, due to the lack of compliance of the SOAP/WSDL specification in the language's library).

This situation prevents these services to be popularized for and used in combination by end users as a infrastructure of the daily research. The  BioMOBY project has been tried to overcome the circumstances by defining ontologies for data types and methods used in the services. However, there are many major service providers which are not yet participated in the BioMOBY framework. Especially, there are several web service providers in Japan such as  DDBJ,  KEGG,  PDBj and  CBRC but none of them are not integrated in any context.

Thus, at  DBCLS, we started to develop a new proxy server which translates user's request for the appropriate web service provider. If all  Open Bio* libraries support BioMOBY and other service providers, interoperability of these services can be significantly improved. Here, we need agreement for the future direction of web services by every web service providers and client developers.

We believe gathering all web service providers to discuss about the standardization of objects and methods among web services, and Open Bio* library developers from different programming languages ( BioPerl,  BioPython,  BioRuby, and  BioJava) to discuss about the implementation of the common infrastructure, must benefit usability and interoperability for the life science in the next era.

For this purpose, we hope to organize a BioHackathon specialized for the web services from four different domains.

  • Web service providers
    • Encourage independent service providers to join the movement of integration and interoperability
      • Increasing the number of SOAP compliant services (tools/databases)
  • Open Bio* developers
    • Utilizing every bioinformatics web services by 4 major computer languages (Perl, Python, Ruby, Java)
      • Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries
  • Workflow client developers
    • Providing various clients to create and execute bioinformatics workflows
      • Connecting seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Sync - Async
  • BioMOBY project developers
    • Standardizing the objects and methods in bioinformatics web services via BioMOBY
      • Discussing about the best solution of the framework and the ontologies for life science


List of tentative meeting topics for the web service providers, the Open Bio* developers, the workflow client developers, and the BioMOBY project:


DBCLS and CBRC will provide ideal environment for discussions and developments.

Check out the KML file for Google Earth.


  • 2008/2/10 (Sun) - Arrival ( Narita airport, Japan)
  • 2008/2/11 (Mon) - Presentations & discussions (Roppongi Academy Hills)
  • 2008/2/12 (Tue) - Hack, hack, hack (CBRC)
  • 2008/2/13 (Wed) - Hack, hack, hack (CBRC)
  • 2008/2/14 (Thr) - Hack, hack, hack (CBRC)
  • 2008/2/15 (Fri) - Hack, hack, hack (CBRC)
  • 2008/2/16 (Sat) - Departure



  •  Hotel Villa Fontaine Shiodome
    • Free broadband Internet connection
    • Free coffee and bread for breakfast
    • You can find convenience stores and the Starbacks coffee nearby
    • Good access to the Ginza shopping street and the Tsukiji market (famous for Sushi restaurants)


  • By train
    • By JR line (JPY 3,110, 75min - fastest)
      • Narita express (Narita to Tokyo station)
      • Yamanote line (Tokyo to Shimbashi station)
    • By Keisei and JR line (JPY 910, 90min - economical)
      • Keisei express (Keisei Narita to Nippori station)
      • JR Yamanote or Keihin Tohoku line (Nippori to Shimbashi JR station)
    • By Keisei and Asakusa subway line (JPY 960, 90min - economical)
      • Keisei express (Keisei Narita to Keisei Takasago or Aoto station)
      • Asakusa line (Keisei Takasago or Aoto to Shimbashi subway station)
    • From Shimbashi (JR or subway) station, you can walk (5min) or take Yurikamome line for 1 station (JPY 180) to Shiodome station (in front of our hotel Villa Fontaine Shiodome)
  • What you should bring with you?
    • Laptop computer
    • Conversion plug for your AC adaptor
    • LAN cable
    • Warm coat (T-shirt is not recommended for February in Japan)
    • Bottle of local liquor to share :)

Initial documents (outdated)

Starting Points

For a complete list of local wiki pages, see TitleIndex.