Version 42 (modified by anonymous, 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 langugages. However, each service uses their own definition of the data types and naming convensions 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 langauge'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 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 web services with every web service providers and client developers.

We believe gathering all web service providers to disucuss 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 in 2008.

  • Encourage independent service providers to join the movement of integration and interoperability
    • How to increase the number of SOAP compliant services (tools/databases)
  • 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
  • Providing various clients to create and execute bioinformatics workflows
    • Connecting seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Async - Sync
  • Standardizing the objects and methods in bioinformatics web services (BioMOBY)
    • Discuss about the best solution of the framework and ontologies for the 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 at the bottom of this page (attachment).


  • 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) - Depature



If you could recommend any appropriate persons from the following groups, please let me know:

  • NCBI web service developers
  • BioPerl, BioPython, and BioJava developers

Initial documents (outdated)

Starting Points

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