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JOpera and XtremWeb-CH in the Virtual EZ-Grid

JOpera and XtremWeb-CH in the Virtual EZ-Grid. Cesare Pautasso Faculty of Informatics University of Lugano (USI), Switzerland http://www.pautasso.info. in vitro. in silico. Variablility and error assessment. Condition A. Significance assessment. Determine parameters for error model.

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JOpera and XtremWeb-CH in the Virtual EZ-Grid

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  1. JOpera and XtremWeb-CHin the Virtual EZ-Grid Cesare Pautasso Faculty of Informatics University of Lugano (USI), Switzerland http://www.pautasso.info

  2. in vitro in silico Variablility and error assessment Condition A Significance assessment Determine parameters for error model Annotate and normalize data likelihood for differential expression for each gene Data Preprocessing MicroArray Scanner wet lab processing Clustering Extract raw spot intensities Determine Expression Pattern Condition B Image processing 1 spot = 1 gene Expression level: Green: A > B Red: A < B Black: A = B Cell population Virtual Laboratory Workflow

  3. Building Virtual Laboratories

  4. Building Virtual Laboratories

  5. Grid Workflow Management Make it easy to build Grid applications composed of multiple jobs “ Provide the scientist with a platform that takes care of all data handling and record keeping chores so that the user can concentrate on the science and not computer science ”

  6. JOpera: Grid Workflow for Eclipse

  7. Drag, Drop and Connect

  8. Run, Monitor, Steer and Debug

  9. A Growing User Community Swiss Institute of Bioinformatics, Swiss National Supercomputing Center, Purdue University, National Center for Supercomputing Applications, Singapore Management University, McGill University, University of Kent , SINTEF (Norway), IWU Fraunhofer (Germany), University of Nebraska…

  10. Why Users Like JOpera • High Level Workflow Language • Data and Control Aspects (Visual Representation) • Recursion, Iteration, Parallelism and Pipelining • Open and Extensible Component Model • Run existing code without changes • Synchronous, Asynchronous, and Streaming interaction • Web services support (Axis, WSIF) • Secure access to remote file systems and hosts (SSH) • Easy to integrate with existing schedulers (e.g. Condor)

  11. Why Users Like JOpera • High Level Workflow Language • Data and Control Aspects (Visual Representation) • Recursion, Iteration, Parallelism and Pipelining • Open and Extensible Component Model • Run existing code without changes • Synchronous, Asynchronous, and Streaming interaction • Web services support (Axis, WSIF) • Secure access to remote file systems and hosts (SSH) • Easy to integrate with existing schedulers (e.g. Condor) • Strong Eclipse Foundation • Platform Independent (Eclipse/Java) • Flexible, Extensible, Modular and Embeddable

  12. Java SSH XML SQL Human Condor • Snippets • XSLT • Methods • XPath Extensible Component Model • Combine in the same workflow jobs implemented using an open and extensible set of technologies JOpera Workflow WSDL

  13. Java SSH XML SQL Condor Human JOpera Workflow • Snippets • XSLT • Methods • XPath WSDL Sharing Workflows as a Service • JOpera processes are automatically published to clients using a variety of access protocols Eclipse RCP Clients WS Clients Web Clients WSDL Java REST

  14. Java SSH XML SQL Human Condor JOpera Workflow • Snippets • XSLT • Methods • XPath WSDL JOpera in the Virtual EZ-Grid Project • Develop a new adapter for the submission of jobs to XtremWeb-CH Grid middleware(WP3 - Task 3.1) XWeb CH

  15. JOpera and XtremWeb-CH • Definition of job submission parameters based on the API of XtremWeb-CH • Development of a JOpera adapter plugin to connect the two systems: • Start the job by submitting it to the Grid middleware • Monitor the job execution • Retrieve the job results (and its success/failure outcome) • Evaluate and test the integrated system on the Virtual EZ-Grid infrastructure

  16. Roadmap 2009 • Swiss National Grid Deployment • ARC/Nordugrid Job Submission • Virtual EZGrid: Integration with XWebCH • Grid Portal for Workflow Monitoring • New Scientific Workflow Applications • Computational Chemistry Workflows • Web 2.0 Mashup Development • RESTful Web Service Composition • Pipelined processing over RSS Feeds

  17. Free Downloadhttp://www.jopera.org/latest More Information http://www.jopera.org/docs/publications

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