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Life Science Grid Middleware in a More Dynamic Environment

Life Science Grid Middleware in a More Dynamic Environment. Milena Radenkovic & Bartosz Wietrzyk The University of Nottingham, UK http://www.mygrid.org.uk. Talk Plan. From Grid middleware to WSRF and WSN myGrid overview Integrating myGrid with WSRF/WSN Future: self-organizing Grids.

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Life Science Grid Middleware in a More Dynamic Environment

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  1. Life Science Grid Middlewarein a More Dynamic Environment Milena Radenkovic & Bartosz Wietrzyk The University of Nottingham, UK http://www.mygrid.org.uk GADA Workshop 1-2 November 2005

  2. Talk Plan • From Grid middleware to WSRF and WSN • myGrid overview • Integrating myGrid with WSRF/WSN • Future: self-organizing Grids GADA Workshop 1-2 November 2005

  3. Web Services • Web services - the application-centric Web • Standards for message exchanges and interfaces • XML based • Programming language and platform independent • Convergence of Grid and Web Services • Web Services and the State • Failure of the Open Grid Service Infrastructure • No modularity • Limited compatibility with existing Web Services • Too object oriented GADA Workshop 1-2 November 2005

  4. WSRF and WSN • Web Service Resource Framework (WSRF) • Generic and open framework for modelling and accessing stateful resources using Web Services • Standardizing the design patterns and message exchanges for expressing state • Instruction set for the Grid [Priol, 2005] • Web Service Notification (WSN) • WSRF based publish/subscribe notification GADA Workshop 1-2 November 2005

  5. Resource modelling in WSRF • Stateful resource + stateless Web Service = WS-Resource • WS address + resource identifier = WS-Resource qualified endpoint reference • Dynamic creation/destruction of resources • The resource state defined by the resource properties document GADA Workshop 1-2 November 2005

  6. Talk Plan • From Grid middleware to WSRF and WSN • myGrid overview • Integrating myGrid with WSRF/WSN • Future: self-organizing Grids GADA Workshop 1-2 November 2005

  7. myGrid • One of the leading EPSRC eScience pilot projects • Open Source Semantic Grid middleware for Bioinformatics • High-level services for data and application integration • resource discovery • distributed query processing • workflow enactment • Additional services supporting scientific method • provenance management • change notification • personalization GADA Workshop 1-2 November 2005

  8. myGrid architecture GADA Workshop 1-2 November 2005

  9. SOAPLAB Web Service SeqHound Service Any Application Web Service e.g. DDBJ BLAST In silico experiments in myGrid Freefluo Freefluo Workflow engine to run workflows Scufl Simple Conceptual Unified Flow Language Taverna Writing, running workflows & examining results SOAPLAB Makes applications available GADA Workshop 1-2 November 2005

  10. Soaplab Service WSDL Web Service BioMOBY Service Local Java Service GADA Workshop 1-2 November 2005

  11. Talk Plan • From Grid middleware to WSRF and WSN • myGrid overview • Integrating myGrid with WSRF/WSN • Future: self-organizing Grids GADA Workshop 1-2 November 2005

  12. myGrid’s stateful components • myGrid Information Repository (MIR) • Data entities • Workflow Enactment • Enactment services • Workflow enactments • myGrid Notification Service GADA Workshop 1-2 November 2005

  13. myGrid Information Repository (MIR) – before WSRF • MIR data model comprises entity types associated with XML schemas • Entities are: • described by attributes • stored in a relational database • accessed through the Web Service interface • Identified by Life Science IDs GADA Workshop 1-2 November 2005

  14. Our model GADA Workshop 1-2 November 2005

  15. Our new data architecture GADA Workshop 1-2 November 2005

  16. myGrid’s stateful components • myGrid Information Repository (MIR) • Data entities • Workflow Enactment • Enactment services • Workflow enactments • myGrid Notification Service GADA Workshop 1-2 November 2005

  17. Our new enactment architecture GADA Workshop 1-2 November 2005

  18. myGrid’s stateful components • myGrid Information Repository (MIR) • Data entities • Workflow Enactment • Enactment services • Workflow enactments • myGrid Notification Service GADA Workshop 1-2 November 2005

  19. myGrid Notification Service • Every WS-Resource can be a notification producer and manage its subscription • Notification Brokers are optional – not necessary for simple deployments • Notification Brokers can: • Aggregate topics from different notification producers to support their discovery • Distribute the task of message delivery to increase its speed and decrease the network congestion GADA Workshop 1-2 November 2005

  20. Why Apache WSRF/Pubscribe? • Increased compatibility with the implemented myGrid components (Java API) • Dynamic creation of WS-Resources • Call-backs for modification of WS-Resources • High portability (compatible with any Java servlet container) • Free and Open Source GADA Workshop 1-2 November 2005

  21. Advantages of the integration • More flexible, distributed and scalable architecture • More scalable, distributed and lightweight notification infrastructure • One coherent interface to all components • Decreased design efforts in the future • Compatibility with any servlet container • Easier integration with third party software and UK’s National Grid Service GADA Workshop 1-2 November 2005

  22. Talk Plan • From Grid middleware to WSRF and WSN • myGrid overview • Integrating myGrid with WSRF/WSN • Future: self-organizing Grids GADA Workshop 1-2 November 2005

  23. Future: self-organizing Grids • Current limitations of myGrid: • Naming scheme depends on the DNS servers • State is only available when the hosting machine is online • Deployment and maintenance requires high administration effort • Our current work: • Using Distributed Hash Tables (DHTs) to provide self-organization • Using self-organized, distributed caching of the state to increase its availability GADA Workshop 1-2 November 2005

  24. Conclusions • Our work is generic and applicable for other existing higher level middleware projects • WSRF/WSN standards are well suited for the complex higher level middleware • However migration may require a significant coding effort GADA Workshop 1-2 November 2005

  25. EPSRC funded UK eScience Program Pilot Project Some slides taken from Carole Goble GADA Workshop 1-2 November 2005

  26. Core • Matthew Addis, Nedim Alpdemir, Tim Carver, Rich Cawley, Neil Davis, Alvaro Fernandes, Justin Ferris, Robert Gaizaukaus, Kevin Glover, Carole Goble, Chris Greenhalgh, Mark Greenwood, Yikun Guo, Jan Humble, Ananth Krishna, Peter Li, Phillip Lord, Darren Marvin, Simon Miles, Luc Moreau, Arijit Mukherjee, Tom Oinn, Juri Papay, Savas Parastatidis, Norman Paton, Terry Payne, Matthew Pocock Milena Radenkovic, Stefan Rennick-Egglestone, Peter Rice, Ian Roberts, Martin Senger, Nick Sharman, Robert Stevens, Victor Tan, Anil Wipat, Paul Watson, Jimi Worthington and Chris Wroe. Users • Simon Pearce and Claire Jennings, Institute of Human Genetics School of Clinical Medical Sciences, University of Newcastle, UK • Hannah Tipney, May Tassabehji, Andy Brass, St Mary’s Hospital, Manchester, UK • Steve Kemp, Liverpool, UK Postgraduates • Martin Szomszor, Duncan Hull, Jun Zhao, Pinar Alper, Keith Flanagan, Antoon Goderis, Tracy Craddock, Alastair Hampshire, Bartosz Wietrzyk Industrial • Dennis Quan, Sean Martin, Michael Niemi, Syd Chapman (IBM) • Robin McEntire (GSK) Collaborators • Keith Decker GADA Workshop 1-2 November 2005

  27. References • Publications on • Home page: www.mrl.nott.ac.uk/~bzw/ • myGrid site: www.mygrid.org.uk GADA Workshop 1-2 November 2005

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