EMBRACE Web Services Taavi Hupponen CSC – Center for Scientific Computing, Finland BOSC 2007

Contents  Introduction to EMBRACE  Motivation for Integration  EMBRACE services  Choice of Technology and Experiences  Summary

Introduction to EMBRACE  EU FP6 Network of Excellence ( ). 16 partners, coordinated by the EBI  Goal: enabling integration and gridification of bioinformatics tools and databases  Enabling integration in practice: providing Web services access for tools and databases 

Motivation for Integration  Integration: communication between programs, making software to work together  Enabling integration in EMBRACE: providing programmatic access to bioinformatics services  Benefits: integrating the functionality of a service into existing software powerful workflow applications efficient and powerful access directly from your own script or code

Services  Databases: EMBL, UniProt, InterPro, Ensembl, ArrayExpress, MSD, SMART, ProDom, JASPAR, UTRdb, PairsDB…  Tools: EMBOSS, ELM, GOblet, SAMOSA, CATHEDRAL, CATHSCAN, SSAP, FUNCUT, palign, prodiv-TMHH, RNAmmer…

Integration Technology: Web Services  Web services: machine to machine communication using web technologies such as HTTP and XML  Reasons platform independency, interoperability – independent service providers, client developers and users wide-spread technology, also outside bioinformatics – existing development tools and specifications  The two common styles for implementing Web services: SOAP based Web services RESTful Web services  The current EMBRACE technology recommendation promotes the use of SOAP

Experiences on SOAP based Web Services

SOAP based Web services  SOAP as the message protocol  WSDL for describing the service interface  WS-* specifications provide further functionality such as security  Web services toolkits help to deal with messy SOAP and WSDL details

Interoperability  Interoperability is about different implementations working together, regardless of the implementation language or platform  Interoperability is essential when the service providers and users are independent  SOAP and WSDL maybe a bit too flexible and somewhat underspecified  possible interoperability issues  Interoperability can be achieved by following guidelines in the WS-I Basic Profile using document literal wrapped style keeping in mind that the wire format is XML

Transferring non-XML data with SOAP  SOAP messages are XML, and the structure information carried with XML is great…  … but XML is not the optimal format for every kind of data, e.g images  Solutions, depending on the size of the data: small: base64 encoding medium: attachments using MTOM/XOP large: – attachments using MTOM/XOP – passing references with SOAP and using external transfer mechanism for the data – streaming is essential in both cases

SOAP Web Services Challenges  SOAP and WSDL are sometimes considered somewhat complex  Capable Web services toolkit and development tools help when dealing with complexity  The features of the available Web services toolkits vary and their use is not without costs learning dependencies more complicated development and build process  Many specifications still developing or not widely supported by toolkits (WSDL-S, MTOM)

SOAP vs REST?  REST is often considered more simple and there is less need for a toolkit  The backend is usually the same, regardless of the interface technology  Regardless of the interface technology, same tasks need to be done (defining data structures, interface description..)  Some SOAP toolkits (e.g. JAX-WS RI) can provided a RESTful interface in addition to a SOAP based one

Summary  EMBRACE is enabling integration of bioinformatics tools and databases by providing Web services access to them  Current technological emphasis is on SOAP based technology, which is a bit complex, but works fine if attention is paid to interoperability and capable tools are used 

Acknowledgements  The EMBRACE project is funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health,“ contract number LHSG-CT