Moby Web Services

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					Moby Web Services
  MSc on Bioinformatics
   for Health Sciences
        May 2006


                          Iván Párraga García
               What are moby webservices?

• Technologically they are            Most common protocol stack in Moby

  standard webservices               Biological Data                 Moby


• Define a new layer on the        Service Description               WSDL

                                      XML Message
  protocol stack to:                                                 SOAP

                                                                     HTTP
                                         Network
   • Have a well known data                                         TCP / IP

     representation based on
     ontology                     Bio-service Publication            Moby

   • Make easier the desired       Service Publication               UDDI
     service discovery
   • Make easier the
     construction of complex      Bio-service Discovery              Moby


     biological workflows (with     Service Discovery                UDDI

     support for error & async
     handling)
                Moby Protocol Interactions

                             Moby
                            Central




                            Internet
3) Service discovery                         2) Service publication




                                                          1) Service development
                       4) Service request

         Service                               Service
          Client       5) Service response     Provider
      The Registry: Moby Central

                   Moby
                  Central




          •   Moby project provides Moby Central as a Perl
              server
                  Internet
          •   It is a directory of services, datatypes and how
              to locate them




Service                                 Service
 Client                                 Provider
                  Client Side

                   Moby
          •   There are different
                  Central           kind of clients
          •   Some of them allow the creation of workflows




                  Internet




Service
 Client       Programmatic                Service
                                          Provider
              libraries:
               Client Side: MOWServ I




• Internet based client
• Discovery of services based on data type
  ontology or on service type ontology
• It allows to connect easily service outputs to
  service inputs
• Interface helps to the Moby object construction
                     Client Side: Mowserv II




Data types and
service ontologies
               Client Side: Mowserv III

                    6) Check results
                                  5) Check execution status

1) Ontology
browsing &
service
selection


2) Input
submission

3) Selection
output name

4) Service
submission
                        Client Side: Mowserv IV




                                                  Integrated HTML
                                                  visualizer

                                     Raw XML         Download
List of available services           visualizer      MOBY object
for this datatype object
Client Side: Taverna I

       • Java based graphical
         integrated workbench
       • It allows the
         construction of
         complex distributed
         workflows
       • It can handle different
         kind of services
         (Moby and others)
Client Side: Taverna II
Processors = Webservices




  Inputs




            Outputs
                       Client Side: Dashboard

                               1) Select client execution tab

2) Select service to
execute



4) Execute service                                 3) Fill up input




5) Check output
                     Client comparison

   Taverna           MOWServ            Dashboard
Easy to build       Hard to build       No workflow
workflows           workflows           support
Discovery of        Discovery of        Discovery of
services based on   services based on   services based on
providers           ontology            ontology
Secondary inputs    Secondary inputs    Secodary inputs
cannot be           can be modified     can be modified
modified
Java program        Web browser         Java program
                    access
                           Client info


• Taverna downloadable at:
  • http://taverna.sourceforge.net/


• MOWServ accessible at:
  • http://www.inab.org/MOWServ/


• Dashboard donwloadable (as part of jMoby) at:
  • http://biomoby.open-bio.org/CVS_CONTENT/moby-
    live/Java/docs/
                 Server Side

                  Moby
          •   Moby provides
                 Central    libraries for easier service
              development in different platforms &
              languages (Perl & Java)




                  Internet

          •   These libraries provide an abstraction of the
              underlayer protocols. The developer does not
              need to handle internet connections or SOAP
              messages and he can concentrate on the
              biological problem
                                        Service
Service                                 Provider
 Client
                 Server Side: jMoby

• For java development
• Hides totally underlayer protocols
• Automatic generation of code (developer
  just needs to concentrate on the biological
  problem)
• Include graphical tools for develop, testing,
  deploy and execution
• Dashboard is part of jMoby
                  Moby on the web

• All the info accessible at the Moby
  homepage at:
  • http://www.biomoby.org/


• All the tools and libraries downloadable via
  CVS (check previous URL for details)
Exercises