News & Topics

Report:Biohackathon 2008

released on 14th Mar, 2008

Biohackathon 2008 was held at CBRC from February 12 to February 15, cosponsored by Database Center for Life Science(DBCLS) in Research Organization of Information and Systems(ROIS). 60 participants in all, including 33 participants from overseas, actively exchanged their opinions and produced beneficial outcome.
The number of web service providers in bioinformatics is increasing in recent years. However, common interfaces cannot often be used since an accessing method frequently varies from site to site. A main purpose of Biohackathon is, therefore, to discuss for standardization as members of such service providers gather in one place.
Participants discussed in groups, focusing on a topic. The topics are mainly as follows:

Biohackathon web site

Main Topics

  • Semantics and Ontology for OpenBio and Web services

    Semantics, protocols, domain models, data types, service types (including BioMoby, etc), and API. In particular the importance of semantics was reconfirmed, and usage of same terms between the services was discussed.

  • Standardization

    Since data types are different in Glycoinformatics, Interaction network, Text mining and Phyloinformatics, standardization was discussed in each field.

  • Asynchronous web services

    Applications, environment and methods were discussed since it is necessary to provide not only synchronous web services but also asynchronous web services.

  • Large data

    Large data frequently needs to be handled in biology. However, there is a problem such as that SOAP cannot handle large data. Handling methods were discussed to address this issue.

  • Security

    Security must be in place in providing web services. Authentication methods, security levels and protection of computer resources were discussed.

  • Service description and discovery

    Discussed were how to appropriately describe services and how the user can quickly locate the services.

  • OpenBio

    Discussed were a standard model for storing and retrieving bio-data in RDBMS (BioSQL) and several existing bio-projects.

Please refer to Biohackathon web site for further details and outcome.

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