Changes between Version 73 and Version 74 of WikiStart

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2008/01/30 13:13:42 (7 years ago)
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hlapp
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    55== Summary == 
    66 
    7 The number of web service providers in bioinformatics field is increasing year by year. 
    8 In theory, these services are interoperable and independent from computer languages. 
     7The number of web service providers in the field of bioinformatics is increasing every year. 
     8In theory, these services are interoperable and independent of specific computer languages. 
    99However, each service uses their own definition of the data types and naming conventions for the methods. 
    1010Moreover, these services are often not usable by specific languages 
    1111(partly, due to the lack of compliance of the SOAP/WSDL specification in the language's library). 
    1212 
    13 This situation prevents these services to be popularized for and used in combination by end users as a infrastructure of the daily research. 
    14 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. 
    15 However, there are many major service providers which are not yet participated in the BioMOBY framework. 
    16 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], 
    17 [http://www.pdbj.org/ PDBj] and [http://www.cbrc.jp/ CBRC] but none of them are not integrated in any context. 
     13This situation prevents these services from becoming popular among and used by end users and developers alike as an infrastructure of their daily research. 
     14The [http://www.biomoby.org/ BioMOBY] project has tried to overcome these problems by defining ontologies for data types and methods used in the services. 
     15However, there are many major service providers which are not yet participating in the BioMOBY framework. 
     16For example, there are several web service providers in Japan such as [http://www.xml.nig.ac.jp/ DDBJ], [http://www.genome.jp/kegg/soap/ KEGG], 
     17[http://www.pdbj.org/ PDBj] and [http://www.cbrc.jp/ CBRC] but none of them are integrated in any way. 
    1818 
    19 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. 
    20 If all [http://www.open-bio.org/ Open Bio*] libraries support BioMOBY and other service providers, interoperability of these services can be significantly improved. 
    21 Here, we need agreement for the future direction of web services by every web service providers and client developers. 
     19Thus, 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 providers. 
     20If all [http://www.open-bio.org/ Open Bio*] libraries support BioMOBY and other service providers, interoperability among these services can be significantly improved. 
     21Here, we need agreement about the future direction of web services by every web service provider and by client developers. 
    2222 
    23 We believe gathering all web service providers to discuss about the standardization of objects and methods among web services, 
     23We believe gathering all web service providers to discuss the standardization of objects and methods among web services, 
    2424and Open Bio* library developers from different programming languages ([http://www.bioperl.org/ BioPerl], [http://www.biopython.org/ BioPython], 
    25 [http://www.bioruby.org/ BioRuby], and [http://www.biojava.org/ BioJava]) to discuss about the implementation of the common infrastructure, 
     25[http://www.bioruby.org/ BioRuby], and [http://www.biojava.org/ BioJava]) to discuss the implementation of the common infrastructure, 
    2626must benefit usability and interoperability for the life science in the next era. 
    2727 
    28 For this purpose, we hope to organize a !BioHackathon specialized for the web services from four different domains. 
     28For this purpose, we hope to organize a !BioHackathon focusing on web services from four different domains. 
    2929 
    3030 * Web service providers 
     
    3232   * Increasing the number of SOAP compliant services (tools/databases) 
    3333 * Open Bio* developers 
    34   * Utilizing every bioinformatics web services by 4 major computer languages (Perl, Python, Ruby, Java) 
     34  * Utilizing every bioinformatics web service by 4 major computer languages (Perl, Python, Ruby, Java) 
    3535   * Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries 
    3636 * Workflow client developers 
     
    3939 * BioMOBY project developers 
    4040  * Standardizing the objects and methods in bioinformatics web services via BioMOBY 
    41    * Discussing about the best solution of the framework and the ontologies for life science 
     41   * Discussing the best solution of the framework and the ontologies for life science 
    4242 
    4343== Topics == 
     
    8181  * Free broadband Internet connection 
    8282  * Free coffee and bread for breakfast 
    83   * You can find convenience stores and the Starbacks coffee nearby 
     83  * You can find convenience stores and the Starbucks coffee nearby 
    8484  * Good access to the Ginza shopping street and the Tsukiji market (famous for Sushi restaurants) 
    8585 
    8686== Access == 
    8787 
    88 How to get from [http://www.narita-airport.jp/ Tokyo Narita International Airport]? 
     88How to get there from [http://www.narita-airport.jp/ Tokyo Narita International Airport]? 
    8989 
    9090 * By bus (JPY 3,000, 90min - easiest, recommended if you bring a heavy suitcase)