| | 1 | = Call for participation for Web Service Hackathon = |
| | 2 | |
| | 3 | Dear all, |
| | 4 | |
| | 5 | Database Center for Life Science (DBCLS) is planning to have a !BioHackathon |
| | 6 | for 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 |
| | 8 | from Japan in total). We can offer your travel fare and accommodation fee |
| | 9 | by the DBCLS budget. |
| | 10 | |
| | 11 | DBCLS (http://dbcls.jp/en/) is a non-profit research institution funded by |
| | 12 | MEXT (http://www.mext.go.jp/english/), established on the April 2007 and |
| | 13 | will continue for the 4 years. One of our goals is to integrate bioinformatics |
| | 14 | web services in a unified and convenient manner. |
| | 15 | |
| | 16 | For this purpose, I'm planning to develop a proxy server which translate |
| | 17 | user's query for appropriate web service provider (e.g. EBI, KEGG, BioMOBY etc.) |
| | 18 | and formalize the returned data structures, so that user can easily build |
| | 19 | their own workflow without bothered by the data format conversion. |
| | 20 | |
| | 21 | This view is partly based on the comment by Tom Oinn in BOSC2007 - even a sequence |
| | 22 | object in BioPerl is not compatible with other Bio* libraries - I strongly agree |
| | 23 | with it. We should define "50 basic bioinformatics data types" and implement them |
| | 24 | by refactoring current Bio* libraries, then use them in every web services. |
| | 25 | |
| | 26 | BioMOBY has been served as a initial repository for various web services, however, |
| | 27 | there are hundreds of data types are listed and many of them are very similar. |
| | 28 | I think they need to be re-organized as the naming convention of the methods and |
| | 29 | data types currently used are extremely diverged. I suppose this situation restrict |
| | 30 | the interoperability of the services, and to develop any bioinformatics workflow, |
| | 31 | user needs to consult with (poor, in some cases) documentations. |
| | 32 | |
| | 33 | So, I hope to gather as many developers as we can, from major web service providers, |
| | 34 | from Bio* developers, and other integrated service providers like BioMOBY and Taverna, |
| | 35 | to discuss and develop a new Open Bio* standard for the web-service-centric |
| | 36 | bioinformatics-nation (TM). |
| | 37 | |
| | 38 | I'm preferentially writing you to hear any input to finalize our objectives of |
| | 39 | the web service hackathon, as my current knowledge on BioMOBY, myGrid, Taverna |
| | 40 | and other web services are very limited. |
| | 41 | |
| | 42 | From my experience as a developer of the BioRuby library and the KEGG API service, |
| | 43 | I'm still stick on the SOAP/WSDL services even though the REST is the current trend. |
| | 44 | Because, |
| | 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 |
| | 50 | |
| | 51 | On behalf of the DBCLS, |
| | 52 | Toshiaki Katayama |
| | 53 | |
