Transcript Introduction to Workflows with Taverna

Tom Oinn, [email protected], 21st May 2007
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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
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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.
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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
Available
services
Workflow
diagram
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.
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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...
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Taverna can interoperate the following by
default :
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SOAP based web services
Biomart data warehouses
Soaplab wrapped command line tools
BioMoby services and object constructors
Inline interpreted scripting (Java based)
Provided by EBI
and covered
in this
workshop
Other service classes can be added through an
extension point (but you probably don’t need to)
•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
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
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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.
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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.
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Result visualization
 Common renderers included in base distribution include 3d structure, images, graph
rendering
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Extensibility
 New service classes
 New renderer types
 New UI elements
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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.
Carole Goble, Norman Paton, Robert Stevens, Anil Wipat, David De Roure, Steve Pettifer
OMII-UK
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Tom Oinn, Daniele Turi, Katy Wolstencroft, June Finch, Stuart Owen, David Withers, Stian Soiland, Franck Tanoh,
Matthew Gamble
Research
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Martin Szomszor, Duncan Hull, Jun Zhao, Pinar Alper, Antoon Goderis, Alastair Hampshire, Qiuwei Yu, Wang
Kaixuan,
Current contributors
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Matthew Pocock, James Marsh, Khalid Belhajjame, PsyGrid project, Bergen people, EMBRACE people
User Advocates and their bosses
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Simon Pearce, Claire Jennings, Hannah Tipney, May Tassabehji, Andy Brass, Paul Fisher, Peter Li, Simon Hubbard,
Tracy Craddock, Doug Kell
Past Contributors
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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
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Dennis Quan, Sean Martin, Michael Niemi (IBM), Chimatica,
Funders
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EPSRC, Wellcome Trust
OMII-UK, eScience All hands meeting 2006