Changes between Initial Version and Version 1 of CallForParticipation

2007/11/21 00:53:40 (12 years ago)



  • CallForParticipation

    v1 v1  
     1= Call for participation for Web Service Hackathon = 
     3Dear all, 
     5Database Center for Life Science (DBCLS) is planning to have a !BioHackathon 
     6for the Web Service in next January or February and hope to invite all of you to Japan 
     7(currently considering upto 20 developers from abroad and other 20 developers 
     8from Japan in total). We can offer your travel fare and accommodation fee 
     9by the DBCLS budget. 
     11DBCLS ( is a non-profit research institution funded by 
     12MEXT (, established on the April 2007 and 
     13will continue for the 4 years. One of our goals is to integrate bioinformatics 
     14web services in a unified and convenient manner. 
     16For this purpose, I'm planning to develop a proxy server which translate 
     17user's query for appropriate web service provider (e.g. EBI, KEGG, BioMOBY etc.) 
     18and formalize the returned data structures, so that user can easily build 
     19their own workflow without bothered by the data format conversion. 
     21This view is partly based on the comment by Tom Oinn in BOSC2007 - even a sequence 
     22object in BioPerl is not compatible with other Bio* libraries - I strongly agree 
     23with it. We should define "50 basic bioinformatics data types" and implement them 
     24by refactoring current Bio* libraries, then use them in every web services. 
     26BioMOBY has been served as a initial repository for various web services, however, 
     27there are hundreds of data types are listed and many of them are very similar. 
     28I think they need to be re-organized as the naming convention of the methods and 
     29data types currently used are extremely diverged. I suppose this situation restrict 
     30the interoperability of the services, and to develop any bioinformatics workflow, 
     31user needs to consult with (poor, in some cases) documentations. 
     33So, I hope to gather as many developers as we can, from major web service providers, 
     34from Bio* developers, and other integrated service providers like BioMOBY and Taverna, 
     35to discuss and develop a new Open Bio* standard for the web-service-centric 
     36bioinformatics-nation (TM). 
     38I'm preferentially writing you to hear any input to finalize our objectives of 
     39the web service hackathon, as my current knowledge on BioMOBY, myGrid, Taverna 
     40and other web services are very limited. 
     42From my experience as a developer of the BioRuby library and the KEGG API service, 
     43I'm still stick on the SOAP/WSDL services even though the REST is the current trend. 
     45 * every SOAP server speaks the same language 
     46  * cost to develop a client code can be minimal 
     47  * user doesn't need any parser (cf. DAS spec etc.) 
     48  * user can easily pass any complex data structure (including <ComplexType>) 
     49 * we can also provide REST service if appropriate 
     51On behalf of the DBCLS, 
     52Toshiaki Katayama