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

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

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

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…

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

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

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

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 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 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

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

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.

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.