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Bringing caBIG services together using Taverna

Aleksandra Nenadic, Stian Soiland-Reyes, Carole Goble University of Manchester 2009-12-07 All Hands Meeting Oxford

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Bringing caBig services together using Taverna,[object Object],Alexandra Nenadic, Stian Soiland-Reyes, Carole Goble,[object Object],University of Manchester,[object Object],All Hands Meeting, Oxford 2009-07-12,[object Object]
What is caBIG?,[object Object],Cancer Biomedical Informatics Grid,[object Object],Biomedical platform by National Cancer Institute (NCI) in US,[object Object],Linking cancer institutes and research organisations across the country,[object Object],Improving the US cancer research communitity’s access to bioinformatics data and tools.,[object Object]
caBIG services,[object Object],~120 service providers across US,[object Object]
caBIG services,[object Object],75 data services,[object Object],53 analytical services,[object Object],Data types semantically described using a controlled vocabolary – Silver level compatibility,[object Object],Services registered in an Index Service, with service metadata (caDSR),[object Object],Security infrastructure (GAARDS), delegation service, single sign-on,[object Object],Thus – forming a grid - caGrid,[object Object]
Taverna workbench,[object Object],Open source workflow authoring and execution tool,[object Object]
Taverna use,[object Object],Used by eScientists in fields such as:,[object Object],Bioinformatics,[object Object],Chemistry and cheminformatics,[object Object],Astronomy,[object Object],Text mining,[object Object],Social sciences,[object Object],Music,[object Object],.. and more,[object Object]
Connecting services,[object Object],Taverna is oblivious to the science, workflows are built by dragging and dropping how the data should flow between different services,[object Object],Web Services,[object Object],Local scripts,[object Object],Java APIs,[object Object],R,[object Object],.. other customized invocation mechanisms,[object Object]
caGrid technology,[object Object],WS-Resource Framework (WSRF) grid services,[object Object],Based on Globus Toolkit,[object Object],Secured services: Extending Grid Security Infrastructure (GSI) to form GAARDS (Grid Authentication and Authorization with Reliable Distributed Services),[object Object]
caGrid extensions to Taverna,[object Object],Browse and semantic search registered caBIG services,[object Object],caBIG single sign-on support through GAARDS,[object Object],Support for WSRF stateful web services,[object Object]
Finding caBIG services from Taverna,[object Object]
caBIG single sign-on,[object Object],Sign in to chosen authentication service,[object Object],Temporary certificate is issued,[object Object],Credentials delegated to calls to grid services,[object Object]
WSRF services,[object Object],Most caBIG services can be invoked as normal WSDL services from Taverna,[object Object],Taverna extension add supports for stateful WS-Resource Framework (WSRF)  services,[object Object],Passing endpoint references as part of the workflow,[object Object]
Integrating Taverna and caBIG,[object Object],Taverna workflow execution as a caGrid WSRF service,[object Object],caTransfer – supporting large data,[object Object],CQL building – customized data queries from within Taverna,[object Object],University of Chicago /  Argonne National Laboratory,[object Object]
Use case: Lymphoma prediction workflow,[object Object]
Use case: Lymphoma prediction workflow,[object Object]
Taverna demonstration,[object Object],Monday 2009-12-07 17:40,[object Object],Thursday 2009-12-10 12:50,[object Object],eScience North West Centre stand  downstairs, booth 6,[object Object]
Questions..?,[object Object]

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  • 14.
  • 15.
  • 16.
  • 17.