| | 7 | Dear all, |
| | 8 | |
| | 9 | Database Center for Life Science (DBCLS) is planning to have a BioHackathon |
| | 10 | for 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 |
| | 12 | from Japan in total). We can offer your travel fare and accommodation fee |
| | 13 | by the DBCLS budget. |
| | 14 | |
| | 15 | DBCLS (http://dbcls.jp/en/) is a non-profit research institution funded by |
| | 16 | MEXT (http://www.mext.go.jp/english/), established on the April 2007 and |
| | 17 | will continue for the 4 years. One of our goals is to integrate bioinformatics |
| | 18 | web services in a unified and convenient manner. |
| | 19 | |
| | 20 | For this purpose, I'm planning to develop a proxy server which translate |
| | 21 | user's query for appropriate web service provider (e.g. EBI, KEGG, BioMOBY etc.) |
| | 22 | and formalize the returned data structures, so that user can easily build |
| | 23 | their own workflow without bothered by the data format conversion. |
| | 24 | |
| | 25 | This view is partly based on the comment by Tom Oinn in BOSC2007 - even a sequence |
| | 26 | object in BioPerl is not compatible with other Bio* libraries - I strongly agree |
| | 27 | with it. We should define "50 basic bioinformatics data types" and implement them |
| | 28 | by refactoring current Bio* libraries, then use them in every web services. |
| | 29 | |
| | 30 | BioMOBY has been served as a initial repository for various web services, however, |
| | 31 | there are hundreds of data types are listed and many of them are very similar. |
| | 32 | I think they need to be re-organized as the naming convention of the methods and |
| | 33 | data types currently used are extremely diverged. I suppose this situation restrict |
| | 34 | the interoperability of the services, and to develop any bioinformatics workflow, |
| | 35 | user needs to consult with (poor, in some cases) documentations. |
| | 36 | |
| | 37 | So, I hope to gather as many developers as we can, from major web service providers, |
| | 38 | from Bio* developers, and other integrated service providers like BioMOBY and Taverna, |
| | 39 | to discuss and develop a new Open Bio* standard for the web-service-centric |
| | 40 | bioinformatics-nation (TM). |
| | 41 | |
| | 42 | I'm preferentially writing you to hear any input to finalize our objectives of |
| | 43 | the web service hackathon, as my current knowledge on BioMOBY, myGrid, Taverna |
| | 44 | and other web services are very limited. |
| | 45 | |
| | 46 | From my experience as a developer of the BioRuby library and the KEGG API service, |
| | 47 | I'm still stick on the SOAP/WSDL services even though the REST is the current trend. |
| | 48 | Because, |
| | 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 |
| | 54 | |
| | 55 | On behalf of the DBCLS, |
| | 56 | Toshiaki Katayama |
| | 57 | |
| 9 | | == Attendee == |
| | 60 | * Tokyo, Japan |
| | 61 | * Candidate dates |
| | 62 | |
| | 63 | 1. 2008/02/10-02/16 |
| | 64 | 2. 2008/01/27-02/02 |
| | 65 | 3. 2008/02/03-02/09 |
| | 66 | |
| | 67 | == Attendees == |
| | 68 | |
| | 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) |
| | 73 | |
| | 74 | If 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 |
