Embrace Web Services

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 (2005-2010). 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
http://www.embracegrid.info

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
http://www.embracegrid.info

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-2004-512092.

Embrace Web Services

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