= !BioHackathon 2008 =

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

== Summary ==

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 [http://www.biomoby.org/ 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 [http://www.xml.nig.ac.jp/ DDBJ], [http://www.genome.jp/kegg/soap/ KEGG],
[http://www.pdbj.org/ PDBj] and [http://www.cbrc.jp/ CBRC] but none of them are not integrated in any context.

Thus, at [http://www.dbcls.jp/en/ DBCLS], we started to develop a new proxy server which translates user's request for the appropriate web service provider.
If all [http://www.open-bio.org/ 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 ([http://www.bioperl.org/ BioPerl], [http://www.biopython.org/ BioPython],
[http://www.bioruby.org/ BioRuby], and [http://www.biojava.org/ 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

== Topics ==

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

 * [wiki:ServiceProvider_workgroup]
 * [wiki:OpenBio_workgroup]
 * [wiki:Workflow_workgroup]
 * [wiki:BioMOBY_workgroup]

== Venue ==

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

 * [http://www.academyhills.com/english/ Roppongi Academy Hills] (Roppongi, Central Tokyo)
 * [http://www.cbrc.jp/index.eng.html CBRC] Computational Biology Research Cener (Odaiba, Tokyo Bay Area)

Check out the KML file for Google Earth at the bottom of this page (attachment).

== Schedule ==

 * 2008/2/10 (Sun) - Arrival ([http://www.narita-airport.jp/en/ 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

== Housing ==

 * [http://www.hvf.jp/eng/shiodome.php Hotel Villa Fontaine Shiodome]

== Attendees ==

 * [wiki:ListOfAttendees]

=== Initial documents (outdated) ===

 * [wiki:CallForParticipation]
 * [wiki:CallForParticipation_in_Japanese]
 * [wiki:Objectives]
 * [wiki:Objectives_in_Japanese]

=== Starting Points ===

 * TracGuide --  Built-in Documentation
 * [http://trac.edgewall.org/ The Trac project] -- Trac Open Source Project
 * [http://trac.edgewall.org/wiki/TracFaq Trac FAQ] -- Frequently Asked Questions
 * TracSupport --  Trac Support

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