BioHackathon 2008

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


The number of web service providers in the field of bioinformatics is increasing every year. In theory, these services are interoperable and independent of specific computer languages. However, each service uses its own definition of data types and method naming conventions. 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 lack of interoperability prevents these services from becoming popular among end users and developers alike and they are under utilised as an infrastructure of their daily research.

The  BioMOBY project has tried to overcome these problems by defining ontologies for data types and methods used in the services. However, there are many major service providers which are not yet participating in the BioMOBY framework. For example, there are several web service providers in Japan such as  DDBJ,  KEGG,  PDBj and  CBRC but none of these are integrated in any way.

For this reason, at  DBCLS, we started to develop a new proxy server which translates user requests for the appropriate web service providers. If all [ Open Bio*] libraries were to support BioMOBY and other service providers, interoperability among these services are significantly improved. To achieve this we need agreement about the future direction of web services by every web service provider and by client developers.

We believe that getting all web service providers together, to discuss the standardization of objects and methods among web services, with Open Bio* library developers from different programming languages ( BioPerl,  BioPython,  BioRuby, and  BioJava) will benefit usability and interoperability of services for the life sciences in the next era.

For this purpose, we organize a BioHackathon focusing on web services from four different domains.

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

Presentations and Open Space topics



Detailed program:

At a glance:

  • 2008-2-10 (Sun) - Arrival ( Narita airport, Japan)
  • 2008-2-11 (Mon) - Presentations & discussions ( Roppongi Academy Hills)
  • 2008-2-12 (Tue) - Hack, hack, hack on the 8th floor & Banquet on the 11th floor ( 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


  •  DBCLS (Database Center for Life Science)
  •  CBRC (Computational Biology Research Center)


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

  •  Roppongi Academy Hills (Roppongi, Central Tokyo)
    • Access from the hotel: Shiodome to Roppongi station - Ooedo subway line (JPY 210, 12min)
  •  CBRC Computational Biology Research Cener (Odaiba, Tokyo Bay Area)
    • Access from the hotel: Shiodome to Telecom center station - Yurikamome line (JPY 370, 17min)
    • One day pass (JPY 800) is recommend, so that you can go out for lunch to the restaurants at the stations nearby

Check out the KML file for the  Google Earth.


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


How to get from  Tokyo Narita International Airport?

  • By bus (JPY 3,000, 90min - easiest, recommended if you bring a heavy suitcase)
    •  Airport Limousine is available to Conrad Tokyo hotel (next to our hotel Villa Fontaine Shiodome)
  • By train
    • By JR line (JPY 3,110, 75min - fastest)
      • Narita to Tokyo station - Narita express
      • Tokyo to Shimbashi station - Yamanote line
    • By Keisei and JR line (JPY 910, 90min - economical)
      • Keisei Narita to Nippori station - Keisei express
      • Nippori to Shimbashi JR station - JR Yamanote or Keihin Tohoku line
    • By Keisei and Asakusa subway line (JPY 960, 90min - economical)
      • Keisei Narita to Keisei Takasago or Aoto station - Keisei express
      • Keisei Takasago or Aoto to Shimbashi subway station - Asakusa line

From Shimbashi (JR or subway) station, you can take Yurikamome line for 1 station (JPY 180) to Shiodome station (in front of our hotel Villa Fontaine Shiodome) or walk (5min).


  • 1 USD (US dollar) is about 105-110 JPY (Japanese yen)

Mailing List

SVN repository

You can access SVN repository using your ID and password:


What you should bring with you?

  • Laptop computer
  • Conversion plug for your AC adaptor (identical to US type; 100 volt)
  • Warm coat (T-shirt is not recommended for February in Japan)
  • Bottle of local liquor to share :)

Photo Album

Streaming ... done

Initial documents (outdated)

Starting Points

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