Taverna

1. Taverna Kevin Benson Guy Rixonhttp://www.vamdc.eu/http://www.taverna.org.uk

2. Taverna and MyExperiment Taverna • Enables the interoperation between databases and tools by providing a toolkit for composing, executing and managing workflow experiments • Access to local and remote resources and analysis tools • Automation of data flow • Iteration over large data sets myExperiment • Workflow sharing and publishing environment

3. Client Applications Provenance Ontology myExperiment Web Portal(now integrated into workbench) Taverna Workbench GUI Workflow Warehouse Provenance Warehouse Service / Component Catalogue Feta/BioCatalogue Information Services Taverna Workflow Enactor LogBook Provenance Management Default Results Service Ontology Custom Datasets 3rd Party Resources (Web Services, Grid Services) Service Management Resources

4. Predicted Genes out Sequence RepeatMasker Web service GenScan Web Service BlastWeb Service Workflows • Workflows provide a general technique for describing and enacting a process • Describes what you want to do, not how you want to do it • Simple language specifies how bioinformatics processes fit together • Processes are represented as web services

5. Workflow diagram Available services Tree view of workflow structure

6. Who Uses Taverna Users worldwide • Systems biology • Proteomics • Gene/protein annotation • Microarray data analysis • Medical image analysis • Heart simulations • High throughput screening • Genotype/Phenotype studies • Health Informatics • Astronomy • Chemoinformatics • Data integration

7. What type of Services • Public/private/secured WSDL/SOAP web services • RESTful web services • Spreadsheet import • Command line tools (local/ssh) • Inline scripts (Beanshell, R) • Java APIs • Customizations: • BioMart, BioMoby / SADI • Soaplab • Grid services (Globus, EGEE gLite, caGrid) • … your tool (Plugin tutorial on wiki)

8. VAMDC with Taverna • Prototype stage in Period 2. • Integrated with SOAPLab to run Applications. • Integrated with Taverna Plug-in system. To run Applications and XSAMS Node.

9. VAMDC with Taverna • Experimentation will commence soon on running these Applications on the Grid. • Taverna already has plugins developed by other communities to run jobs on a Grid. VAMDC will investigate the usage of these plugins. • Prototype released to a few individuals and to be released to beta testers by end of September. • Delivery of VAMDC integration with Taverna in Period 3. Workflows will use the myExperiment website to help users with running various workflows. • Collaboration with Pierre Le Sidaner to have Taverna worflows calling applications installed on the Grid.

10. Vamdc Plugin XSTAR App Service being ran then fed into TopCat.

11. MyExperiment for Sharinghttp://www.myexperiment.org/ • myExperiment can provide a central location for workflows from one community/group • myExperiment allows you to say • Who can look at your workflow • Who can download your workflow • Who can modify your workflow • Who can run your workflow • Share individual workflows or packs – collections of workflows and/or associated data / documentation

12. Taverna Summary • Taverna • Workflow design and execution environment • Access to local and remote resources and analysis tools • Automation of data flow • Iteration over large data sets • Used by 350+ organisations • myExperiment • Workflow sharing and publishing environment • Web 2.0 • Social network • Sharing workflows, expertise, knowledge and/or data • >5000users • 1979workflows

13. VAMDc with Taverna Summary • Prototype to be released to a broader set of beta testers by end of September 2011. • Continue Development and Improvements to the VAMDC plugin during Period 3. • Collaborate with Pierre Lesidaner to run a focused set of Applications on the Grid. • Build up a set of Workflows for the VAMDC communities to easily share and collaborate, with the use of the myExperiment website. • Release in Period 3.

14. myGrid acknowledgements • With Several slides coming from the presentation by ‘Katy Wolstencroft’ from a 2008 presentation: • http://www.mygrid.org.uk/outreach/presentations/presentation-wolstencroft2008b/ • Carole Goble, Norman Paton, Robert Stevens, Anil Wipat, David De Roure, Steve Pettifer • OMII-UK and myExperiment Tom Oinn, Katy Wolstencroft, Daniele Turi, June Finch, Stuart Owen, David Withers, Stian Soiland, Franck Tanoh, Matthew Gamble, Alan Williams, Ian Dunlop, Alex Nenadic, Jiten Bhagat, Don Cruickshank, Sergejs Aleksejevs • 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, Marco Roos, Matthew Pocock, Mark Wilkinson • 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. • IndustrialDennis Quan, Sean Martin, Michael Niemi (IBM), Chimatica. • Funding EPSRC, Wellcome Trust.