Changes between Version 12 and Version 13 of WikiStart

2007/11/21 00:53:12 (15 years ago)



  • WikiStart

    v12 v13  
    1010 * [wiki:CallForParticipation] 
    12 Dear all, 
    14 Database Center for Life Science (DBCLS) is planning to have a !BioHackathon 
    15 for the Web Service in next January or February and hope to invite all of you to Japan 
    16 (currently considering upto 20 developers from abroad and other 20 developers 
    17 from Japan in total). We can offer your travel fare and accommodation fee 
    18 by the DBCLS budget. 
    20 DBCLS ( is a non-profit research institution funded by 
    21 MEXT (, established on the April 2007 and 
    22 will continue for the 4 years. One of our goals is to integrate bioinformatics 
    23 web services in a unified and convenient manner. 
    25 For this purpose, I'm planning to develop a proxy server which translate 
    26 user's query for appropriate web service provider (e.g. EBI, KEGG, BioMOBY etc.) 
    27 and formalize the returned data structures, so that user can easily build 
    28 their own workflow without bothered by the data format conversion. 
    30 This view is partly based on the comment by Tom Oinn in BOSC2007 - even a sequence 
    31 object in BioPerl is not compatible with other Bio* libraries - I strongly agree 
    32 with it. We should define "50 basic bioinformatics data types" and implement them 
    33 by refactoring current Bio* libraries, then use them in every web services. 
    35 BioMOBY has been served as a initial repository for various web services, however, 
    36 there are hundreds of data types are listed and many of them are very similar. 
    37 I think they need to be re-organized as the naming convention of the methods and 
    38 data types currently used are extremely diverged. I suppose this situation restrict 
    39 the interoperability of the services, and to develop any bioinformatics workflow, 
    40 user needs to consult with (poor, in some cases) documentations. 
    42 So, I hope to gather as many developers as we can, from major web service providers, 
    43 from Bio* developers, and other integrated service providers like BioMOBY and Taverna, 
    44 to discuss and develop a new Open Bio* standard for the web-service-centric 
    45 bioinformatics-nation (TM). 
    47 I'm preferentially writing you to hear any input to finalize our objectives of 
    48 the web service hackathon, as my current knowledge on BioMOBY, myGrid, Taverna 
    49 and other web services are very limited. 
    51 From my experience as a developer of the BioRuby library and the KEGG API service, 
    52 I'm still stick on the SOAP/WSDL services even though the REST is the current trend. 
    53 Because, 
    54  * every SOAP server speaks the same language 
    55   * cost to develop a client code can be minimal 
    56   * user doesn't need any parser (cf. DAS spec etc.) 
    57   * user can easily pass any complex data structure (including <ComplexType>) 
    58  * we can also provide REST service if appropriate 
    60 On behalf of the DBCLS, 
    61 Toshiaki Katayama 
    6312== Venue ==