Changes between Version 6 and Version 7 of CallForParticipation

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2007/12/10 23:54:26 (10 years ago)
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anonymous
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  • CallForParticipation

    v6 v7  
    11= Call for participation for Web Service Hackathon = 
    2  
    3  * [wiki:CallForParticipation200711] 
    42 
    53Dear all, 
    64 
    7 Database Center for Life Science (DBCLS) is planning to have a !BioHackathon 
    8 for the Web Service in next January or February and hope to invite all of you to Japan 
    9 (currently considering upto 20 developers from abroad and other 20 developers 
    10 from Japan in total). We can offer your travel fare and accommodation fee 
    11 by the DBCLS budget. 
     5I would like to invite you to Japan for the BioHackathon specialized for the web services. 
    126 
    13 DBCLS (http://dbcls.jp/en/) is a non-profit research institution funded by 
    14 MEXT (http://www.mext.go.jp/english/), established on the April 2007 and 
    15 will continue for the 4 years. One of our goals is to integrate bioinformatics 
    16 web services in a unified and convenient manner. 
     7 Place: Tokyo, Japan 
     8 Dates: 2008/Feb/10(Sun) - 16(Sat) 
     9 Details: http://hackathon.dbcls.jp/ 
    1710 
    18 For this purpose, I'm planning to develop a proxy server which translate 
    19 user's query for appropriate web service provider (e.g. EBI, KEGG, BioMOBY etc.) 
    20 and formalize the returned data structures, so that user can easily build 
    21 their own workflow without bothered by the data format conversion. 
     11Database Center for Life Science (DBCLS; http://dbcls.jp/en/) is planning to have a BioHackathon for the Web Service in next February and hope to invite of you to Japan (currently considering upto 20 developers from abroad and other 20 developers from Japan in total). We can offer your travel fare and accommodation fee by the DBCLS budget. 
    2212 
    23 This view is partly based on the comment by Tom Oinn in BOSC2007 - even a sequence 
    24 object in BioPerl is not compatible with other Bio* libraries - I strongly agree 
    25 with it. We should define "50 basic bioinformatics data types" and implement them 
    26 by refactoring current Bio* libraries, then use them in every web services. 
     13DBCLS is a non-profit research institution funded by MEXT (http://www.mext.go.jp/english/), established on the April 2007 and will continue for the 4 years. Our main goal is to integrate life science resources especially in Japan, and web service is one of the key technology to accomplish this purpose. 
    2714 
    28 BioMOBY has been served as a initial repository for various web services, however, 
    29 there are hundreds of data types are listed and many of them are very similar. 
    30 I think they need to be re-organized as the naming convention of the methods and 
    31 data types currently used are extremely diverged. I suppose this situation restrict 
    32 the interoperability of the services, and to develop any bioinformatics workflow, 
    33 user needs to consult with (poor, in some cases) documentations. 
     15We have learned that the BioMOBY project have actively been developed a integrated framework for this purpose, however, most of the Japanese and some of major foreign web service providers not yet follow the movement. 
    3416 
    35 So, I hope to gather as many developers as we can, from major web service providers, 
    36 from Bio* developers, and other integrated service providers like BioMOBY and Taverna, 
    37 to discuss and develop a new Open Bio* standard for the web-service-centric 
    38 bioinformatics-nation (TM). 
     17From my experience as a developer of the BioRuby library and the KEGG API service, I think there still are several problems to create integrated and interoperable environment: 
    3918 
    40 I'm preferentially writing you to hear any input to finalize our objectives of 
    41 the web service hackathon, as my current knowledge on BioMOBY, myGrid, Taverna 
    42 and other web services are very limited. 
     19* How to integrate non-BioMOBY service providers for the future of life science? 
     20* What kind of effort can be made for Open Bio* libraries (BioPerl, BioPython, BioRuby, BioJava) to be interoperable? 
     21* What kind of problems and bottlenecks exist to develop bioinformatics workflows? 
     22* Does every providers agree that the current BioMOBY implementation is the best solution to migrate? 
    4323 
    44 From my experience as a developer of the BioRuby library and the KEGG API service, 
    45 I'm still stick with the SOAP/WSDL services even though the REST is the current trend. 
    46 Because, 
    47  * every SOAP server speaks the same language 
    48   * cost to develop a client code can be minimal 
    49   * user doesn't need any parser (cf. DAS spec etc.) 
    50   * user can easily pass any complex data structure (including <ComplexType>) 
    51  * we can also provide REST service if appropriate 
     24So, in this opportunity, I hope to gather as many developers as we can, from major web service providers, from Bio* developers, from workflow client developers, and from the BioMOBY project, to discuss and develop a new Open Bio* standard for the web-service-centric bioinformatics-nation (TM). 
    5225 
    53 On behalf of the DBCLS, 
     26Regards, 
    5427 
    55 Toshiaki Katayama 
     28Toshiaki Katayama, on behalf of the DBCLS. 
    5629 
    5730-- 
     
    7245 
    7346http://www.genome.jp/kegg/soap/ (KEGG API) 
     47 
     48 * [wiki:CallForParticipation200711] 
     49