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Taverna: From Biology to Astronomy

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  1. Taverna: From Biology to Astronomy Dr Katy Wolstencroft University of Manchester myGrid OMII-UK

  2. What is Taverna? • An environment for workflow design and execution • User interface to a larger suite of middleware – myGrid • Designed to support in silico experiments in biology • Open source

  3. OMII Open Middleware Infrastructure Institute • University of Manchester joined with the Universities of Edinburgh and Southampton in March 2006 • OMII-UK aims to provide software and support to enable a sustained future for the UK e-Science community and its international collaborators. • A guarantee of development and support

  4. The Life Science Community In silico Biology is an open Community • Open access to data • Open access to resources • Open access to tools • Open access to applications Global in silico biological research

  5. The Community Problems • Everything is Distributed • Data, Resources and Scientists • Heterogeneous data • Very few standards • I/O formats, data representation, annotation • Everything is a string! Integration of data and interoperability of resources is difficult

  6. Lots of Resources NAR 2007 – 968 databases

  7. Traditional Bioinformatics 12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt 12241 cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt 12301 gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct 12361 gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt 12421 taggtgactt gcctgttttt ttttaattgg gatcttaatt tttttaaatt attgatttgt 12481 aggagctatt tatatattct ggatacaagt tctttatcag atacacagtt tgtgactatt 12541 ttcttataag tctgtggttt ttatattaat gtttttattg atgactgttt tttacaattg 12601 tggttaagta tacatgacat aaaacggatt atcttaacca ttttaaaatg taaaattcga 12661 tggcattaag tacatccaca atattgtgca actatcacca ctatcatact ccaaaagggc 12721 atccaatacc cattaagctg tcactcccca atctcccatt ttcccacccc tgacaatcaa 12781 taacccattt tctgtctcta tggatttgcc tgttctggat attcatatta atagaatcaa

  8. Workflows as a Solution • Describes whatyou want to do, not how you want to do it • High level description of the experiment • Easier to explain, share, relocate, reuse and repurpose. • Workflow <=> Model • Workflow is the integrator of knowledge • The METHODS section of a scientific publication

  9. Taverna Workflow Components Scufl Simple Conceptual Unified Flow Language

  10. Taverna in an Open World • Open domain services and resources. • Taverna accesses 3000+ services • Third party – we don’t own them – we didn’t build them • All the major providers • NCBI, DDBJ, EBI … • Enforce NO common data model. • Quality Web Services considered desirable

  11. What can you do with myGrid? • ~33,000 downloads • Users worldwide US, Singapore, UK, Europe, Australia • 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

  12. WBSCR21 WBSCR27 WBSCR24 WBSCR14 WBSCR18 WBSCR22 WBSCR28 CLDN3 CLDN4 STX1A ELN CTA-315H11 CTB-51J22 RP11-148M21 RP11-731K22 RP11-622P13 314,004bp extension All nine known genes identified (40/45 exons identified) Examples – Early PioneersWilliams-Beuren Syndrome Identifying new human genome sequence and genes contained within in an area of the genome associated with the disease Improve understanding between genotype and phenotype Four workflow cycles totalling ~ 10 hours The gap was correctly closed and all known features identified

  13. Trypanosomiasis in Africa • Resistance to parasites in different breeds of cattle • Involves: • Microarray analysis • Classical genetics • Biochemical pathway analysis Large data sets, large results sets http://www.genomics.liv.ac.uk/tryps/trypsindex.html

  14. Is Taverna Just for Biologists? • Nothing in the code is specific to biology • The default list of services ARE bio services, but Taverna doesn’t care what they are • Services from other science disciplines can simply be slotted in

  15. Other Examples • Medical imaging • MIAS-GRID –investigating cartilage thickness during drug trials • 2D and 3D brain image registration • Chemoinformatics • CDK-Taverna – project to provide the CDK chemoinformatics tool set as web services • Chimatica - Virtual Drug Candidate Production Environment • Health informatics • PsyGrid – investigating first episode psychosis

  16. Dilbert ##

  17. What Taverna Gives you • Automation • Implicit iteration • Implicit parallelisation • Support for nested workflow construction • Error handling • Retry, failover and automatic substitution of alternates

  18. Extensibility • Accepts many types of services: - web services, beanshell scripts, local java scripts, JDBC connections…etc • Easy to add your own services • Plug-in architecture Easy to build new processor types Easy to extend to include alternative results viewers

  19. Could Taverna be used for Astronomy? • Lots of data (although individual data items might be bigger) • Distributed data • Chains of analyses • MORE standards for data formatting/exchange Investigated by AstroGrid and SAMPO

  20. Sampo - European Southern Observatory project Workflows for data reduction Reasons for choosing Taverna  Open source  Free  Allows customisation  Easy to use and adapt  Designed for science  Most workflow engines are meant for business applications  Very robust  Actively developed  Good support for web services

  21. AstroGrid Workflows Evaluation of Taverna Building plug-ins for AstroGird project In the process of gathering AstroGrid requirements Still things to address……..

  22. Coming soon…Taverna 2 A complete redesign of Taverna from the ground up to enable: • Streaming data • Management of large volumes of data • Better remote workflow execution • Integration with grid resources • Monitoring and steering Beta release due end summer 2007

  23. myGrid acknowledgements Carole Goble, Norman Paton, Robert Stevens, Anil Wipat, David De Roure, Steve Pettifer • OMII-UK Tom Oinn, Katy Wolstencroft, Daniele Turi, June Finch, Stuart Owen, David Withers, Stian Soiland, Franck Tanoh, Matthew Gamble, Alan Williams • 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.