Changes between Version 3 and Version 4 of WikiStart

2007/11/19 12:08:50 (15 years ago)



  • WikiStart

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    55== Objectives == 
     7Dear all, 
     9Database Center for Life Science (DBCLS) is planning to have a BioHackathon 
     10for the Web Service in next January or February and hope to invite all of you to Japan 
     11(currently considering upto 20 developers from abroad and other 20 developers 
     12from Japan in total). We can offer your travel fare and accommodation fee 
     13by the DBCLS budget. 
     15DBCLS ( is a non-profit research institution funded by 
     16MEXT (, established on the April 2007 and 
     17will continue for the 4 years. One of our goals is to integrate bioinformatics 
     18web services in a unified and convenient manner. 
     20For this purpose, I'm planning to develop a proxy server which translate 
     21user's query for appropriate web service provider (e.g. EBI, KEGG, BioMOBY etc.) 
     22and formalize the returned data structures, so that user can easily build 
     23their own workflow without bothered by the data format conversion. 
     25This view is partly based on the comment by Tom Oinn in BOSC2007 - even a sequence 
     26object in BioPerl is not compatible with other Bio* libraries - I strongly agree 
     27with it. We should define "50 basic bioinformatics data types" and implement them 
     28by refactoring current Bio* libraries, then use them in every web services. 
     30BioMOBY has been served as a initial repository for various web services, however, 
     31there are hundreds of data types are listed and many of them are very similar. 
     32I think they need to be re-organized as the naming convention of the methods and 
     33data types currently used are extremely diverged. I suppose this situation restrict 
     34the interoperability of the services, and to develop any bioinformatics workflow, 
     35user needs to consult with (poor, in some cases) documentations. 
     37So, I hope to gather as many developers as we can, from major web service providers, 
     38from Bio* developers, and other integrated service providers like BioMOBY and Taverna, 
     39to discuss and develop a new Open Bio* standard for the web-service-centric 
     40bioinformatics-nation (TM). 
     42I'm preferentially writing you to hear any input to finalize our objectives of 
     43the web service hackathon, as my current knowledge on BioMOBY, myGrid, Taverna 
     44and other web services are very limited. 
     46From my experience as a developer of the BioRuby library and the KEGG API service, 
     47I'm still stick on the SOAP/WSDL services even though the REST is the current trend. 
     49 * every SOAP server speaks the same language 
     50  * cost to develop a client code can be minimal 
     51  * user doesn't need any parser (cf. DAS spec etc.) 
     52  * user can easily pass any complex data structure (including <ComplexType>) 
     53 * we can also provide REST service if appropriate 
     55On behalf of the DBCLS, 
     56Toshiaki Katayama 
    758== Venue == 
    9 == Attendee == 
     60 * Tokyo, Japan 
     61 * Candidate dates 
     63 1. 2008/02/10-02/16 
     64 2. 2008/01/27-02/02 
     65 3. 2008/02/03-02/09 
     67== Attendees == 
     69 * Toshiaki Katayama (Univ of Tokyo, Japan; BioRuby, KEGG API, KEGG DAS) 
     70 * Alberto Labarga (Integromics, Spain; ex-EBI) 
     71 * Matthew Pocock (Newcastle, UK; Taverna, BioJava) 
     72 * Sophia Ananiadou (Manchester, UK; Text mining) 
     74If you could recommend any appropriate persons from the following groups, please let me know: 
     75 * NCBI web service developers 
     76 * BioMOBY service developers (I found some interesting providers in Spain) 
     77 * BioPerl, BioPython, and BioJava developers 
    1179== Starting Points ==