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Introduction to Workflows with Taverna

Tom Oinn, tmo@ebi.ac.uk , 21 st May 2007. Introduction to Workflows with Taverna. For those with wi-fi and little patience. Project homepage : http://taverna.sf.net my Grid project page : http://www.mygrid.org.uk OMII-UK home : http://www.omii.ac.uk

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Introduction to Workflows with Taverna

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  1. Tom Oinn, tmo@ebi.ac.uk, 21st May 2007 Introduction to Workflows with Taverna

  2. For those with wi-fi and little patience... • Project homepage : http://taverna.sf.net • myGrid project page : http://www.mygrid.org.uk • OMII-UK home : http://www.omii.ac.uk • Alberto’s Taverna + EBI mini tutorial : http://www.ebi.ac.uk/Tools/webservices/tutorials/taverna

  3. What is Taverna? • Taverna is : • A workflow language based on a dataflow model. • A graphical editing environment for that language. • An invocation system to run instances of that language on data supplied by a user of the system. • When you download it you get all this rolled into a single piece of desktop software • The enactor can be run independently of the GUI

  4. Workflow diagram Available services Biomart query Soaplab operation wrapping an EMBOSS tool Tree view of workflow structure Version 1.5.1 Shown running on a Mac but written in Java, Runs & developed on Windows, OS X and Linux.

  5. Why do I care? • This meeting presents computationally accessible services. • Taverna is designed to combine these (and other) services into workflows. • Useful when you wish to use the output of a service as input to another one. • Handles parallelism, threading, monitoring, service discovery...

  6. Services • Taverna can interoperate the following by default : • SOAP based web services • Biomart data warehouses • Soaplab wrapped command line tools • BioMoby services and object constructors • Inline interpreted scripting (Java based) • Other service classes can be added through an extension point (but you probably don’t need to) Provided by EBI and covered in this workshop

  7. Biomart Support

  8. Stateful SOAP service support • Add service to services list by pointing Taverna to Web Service Description Language (WSDL) document online • Taverna inspects WSDL, extracts operations • Add operations to workflow, right click to automatically add document builders and splitters for doc/literal style services • Use nested workflow to define polling logic, sub-workflow fails, waits and retries if data is not ready Document builders Service invocation (creates job) Polling loop (check status, fail if not ready) Get results *SOAP is the Simple Object Access Protocol - http://www.w3.org/TR/soap/ & http://www.w3.org/TR/wsdl

  9. Soaplab Support Individual tool within category Soaplab server in services list Soaplab services support rich descriptive metadata • Soaplab services are added to the services palette by pointing Taverna at the root of the Soaplab installation. • Individual services within that server are categorized and displayed within categories • Services support polling and provide links to metadata directly within Taverna • http://www.ebi.ac.uk/Tools/webservices/soaplab/guide

  10. Taverna also provides: • Service discovery • Free text search over ‘known’ services. • Semantic search over service repository, relies on manual service annotation and submission of those annotations to the repository. • Provenance tracking • Lineage tracking of result data. • Automatic semantic annotation of data from service annotations. • Possible as the workflow engine creates a ‘managed environment’ with an overview of all data movement. • Result visualization • Common renderers included in base distribution include 3d structure, images, graph rendering • Extensibility • New service classes • New renderer types • New UI elements

  11. Project management • Funded through the Open Middleware Infrastructure Institute (OMII-UK) as part of the myGrid project run by Carole Goble • Four years old, funding secured through 2008 and beyond. • Development team at Manchester, UK • Wide group of ‘friends and allies’ across the world particularly within UK eScience • Implemented in Java, released under LGPL licence.

  12. myGrid Acknowledgements Carole Goble, Norman Paton, Robert Stevens, Anil Wipat, David De Roure, Steve Pettifer OMII-UK • Tom Oinn, Daniele Turi, Katy Wolstencroft, June Finch, Stuart Owen, David Withers, Stian Soiland, Franck Tanoh, Matthew Gamble Research • Martin Szomszor, Duncan Hull, Jun Zhao, Pinar Alper, Antoon Goderis, Alastair Hampshire, Qiuwei Yu, Wang Kaixuan, Current contributors • Matthew Pocock, James Marsh, Khalid Belhajjame, PsyGrid project, Bergen people, EMBRACE people User Advocates and their bosses • Simon Pearce, Claire Jennings, Hannah Tipney, May Tassabehji, Andy Brass, Paul Fisher, Peter Li, Simon Hubbard, Tracy Craddock, Doug Kell Past Contributors • Matthew Addis, Nedim Alpdemir, Tim Carver, Rich Cawley, Neil Davis, Alvaro Fernandes, Justin Ferris, Robert Gaizaukaus, Kevin Glover, Chris Greenhalgh, Mark Greenwood, Yikun Guo, Ananth Krishna, Phillip Lord, Darren Marvin, Simon Miles, Luc Moreau, Arijit Mukherjee, Juri Papay, Savas Parastatidis, Milena Radenkovic, Stefan Rennick-Egglestone, Peter Rice, Martin Senger, Nick Sharman, Victor Tan, Paul Watson and Chris Wroe. Industrial • Dennis Quan, Sean Martin, Michael Niemi (IBM), Chimatica, Funders • EPSRC, Wellcome Trust OMII-UK, eScience All hands meeting 2006

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