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BioHackathon 2008
Towards integrated web service in life science with Open Bio* libraries.
Summary
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 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 from becoming popular among and used by end users and developers alike 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 them are integrated in any way.
Thus, at DBCLS, we started to develop a new proxy server which translates user's request for the appropriate web service providers. If all Open Bio* libraries support BioMOBY and other service providers, interoperability among these services can be significantly improved. Here, we need agreement about the future direction of web services by every web service provider and by client developers.
We believe gathering all web service providers to discuss 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 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 focusing on 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)
- Encourage independent service providers to join the movement of integration and interoperability
- Open Bio* developers
- Utilizing every bioinformatics web service by 4 major computer languages (Perl, Python, Ruby, Java)
- Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries
- Utilizing every bioinformatics web service by 4 major computer languages (Perl, Python, Ruby, Java)
- Workflow client developers
- Providing various clients to create and execute bioinformatics workflows
- Connecting seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Sync - Async
- Providing various clients to create and execute bioinformatics workflows
- BioMOBY project developers
- Standardizing the objects and methods in bioinformatics web services via BioMOBY
- Discussing the best solution of the framework and the ontologies for life science
- Standardizing the objects and methods in bioinformatics web services via BioMOBY
Topics
List of tentative meeting topics for the web service providers, the Open Bio* developers, the workflow client developers, and the BioMOBY project:
Participants
Schedule
- 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
Venue
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 Google Earth.
Housing
- 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)
Access
How to get there 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
- By JR line (JPY 3,110, 75min - fastest)
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).
Currency
- 1 USD (US dollar) is about 105-110 JPY (Japanese yen)
Misc
What you should bring with you?
- Laptop computer
- Conversion plug for your AC adaptor (identical to US type; 100 volt)
- LAN cable
- Warm coat (T-shirt is not recommended for February in Japan)
- Bottle of local liquor to share :)
Initial documents (outdated)
Starting Points
- TracGuide -- Built-in Documentation
- The Trac project -- Trac Open Source Project
- Trac FAQ -- Frequently Asked Questions
- TracSupport -- Trac Support
For a complete list of local wiki pages, see TitleIndex.
Attachments
- BioHackathon2008Tokyo.kmz (4.1 KB) - added by anonymous 17 years ago.
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CBRCMap.pdf
(212.0 KB) - added by yy
17 years ago.
Map of CBRC (venue after the 2nd day) and spots to visit nearby.
- CBRCMap.ppt (361.0 KB) - added by atsuko 17 years ago.
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biohackathon-schedule.pdf
(52.9 KB) - added by atsuko
17 years ago.
Detailed schedule
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pic_0055.jpg
(8.4 KB) - added by atsuko
17 years ago.
Adaptor plug left behind