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Integrating Scientific Workflows and Large Tiled Display Walls: Bridging the Visualization Divide

Integrating Scientific Workflows and Large Tiled Display Walls: Bridging the Visualization Divide . David Abramson & Hoang Anh Nguyen. Monash University. Outline. Background Scientific Workflow Tiled Display Wall Why do we need a SWF-TDW link ? Design and Implementation Case Study

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Integrating Scientific Workflows and Large Tiled Display Walls: Bridging the Visualization Divide

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  1. Integrating Scientific Workflows and Large Tiled Display Walls: Bridging the Visualization Divide David Abramson & Hoang Anh Nguyen Monash University

  2. Outline • Background • Scientific Workflow • Tiled Display Wall • Why do we need a SWF-TDW link ? • Design and Implementation • Case Study • Conclusions & Future works

  3. Scientific Workflow (SWF) • In-silico science (e-Science) • Complex process • Multiple steps in different computing environment • Scientific workflows • Help automate, manage and execute steps • Provide a high level, robust, repeatable research environment.

  4. Scientific Workflow (SWF) • SWF technology • Application of workflow technology to solve scientific problems [1] • Different from Business Workflow • SWF Management System (SWFMS) • Specification, modification, run, re-run, and monitoring of workflows • Number of SWFMSs: Kepler, Taverna, Triana, Vistrails, etc. • Kepler was chosen to implement our prototype

  5. Kepler SWFMS • Built on top of Ptolemy II • Actor-oriented modelling • Vergil user-interface • Actor-oriented • Actors with input/output ports • Director • Powerful SWFMS • Web and grid-services support • Provenance information

  6. Kepler SWF Figure 1: Sample Workflow in Kepler (source: [2])‏

  7. Tiled Display Wall (TDW) • What is a TDW ? • Visualization cluster • Multiple displays controlled by a powerful computer/cluster • Acts like one or many virtual displays • TDW could be • Projectors • LCDs

  8. Tiled Display Wall (TDW) Figure 2: Scalable Display Wall view from the back (Source [3])‏

  9. Tiled Display Wall (TDW) Figure 3: An Optiportal at Monash Clayton ( Source [4] )‏

  10. Optiportal TDW • Built on top of Rocks • Using SAGE, CGLX, COVISE as rendering middleware • SAGE: Scalable Adaptive Graphics Environment • Open source • Distributed architecture: decouple graphic rendering and graphic display

  11. SAGE UI Client UI Client Pixel stream SAGE messages Free Space Manager Sage receiver Sage receiver Sage receiver SAIL SAIL SAIL SAIL: Sage Application Interface Library App 1 App 2 App 3 Figure 4: SAGE architecture

  12. Why do we need a TDW-SWF link? • Natural marriage • Computation and visualization • To date, no easy method connecting SWF to TDW. • Manual process • Did not receive a lot of attention from workflow community

  13. Design • Goals: • Provide seamless link between SWFs and TDW • Middleware independence • Future user interactions • Design Alternatives • SSH actor • SAGE actor • Distributed architecture: dedicated server

  14. SSH actor • Simple • Inflexible SSH protocol SSH Actor Figure 5: Solution using SSH actor

  15. UI Client SAGE actor UI Client Free Space Manager messages Pixel stream Sage receiver Sage receiver Sage receiver • compact • possible feeding user feedbacks to workflow • intensive computation on machine running Kepler • middleware dependent SAIL App SAIL SAIL JNI Kepler code (Java) Figure 6: SAGE actor block diagram SAGE actor

  16. Dedicated server OptIPortal Middleware OptIPortal Middleware Server Interface Server Interface OptIPortal Middleware • middleware-independent • highly distributed • small communication overhead OptiServer Server Interface OptIPortal Kepler OptIPortal Actor Figure 7: Distributed Architecture‏

  17. Prototype Implementation Free Space Manager messages Pixel stream Sage receiver Sage receiver Sage receiver SAIL SAIL SAIL App 1 App 2 App 3 OptiUI Client OptiServer Figure 8: Implementation Kepler OptIPortal Actor

  18. CASE STUDY • Illustrate the ease of use with OptiportalActor • Use OptiportalActor in a set of optical microscopy workflows • To visualize images of antibody cancer therapies* • Part of a larger project • Virtual microscopy • Demonstrating the utility of workflows for microscopy

  19. Antibody cancer therapies* • Developed in the Faculty of Medicine, Monash University • Fluorescent labeled antibodies, together with various reagents, are used to mark three distinct tissue types: • tumour nuclei • “stroma” or connective tissue • blood vessels that feed the tumour • These therapies work by denaturing the blood vessels to the tumor

  20. Antibody cancer therapies* Nuclei Blood vessels Figure 9: Cancer Nuclei, Blood vessels, Stroma in confocal microscopy Merged image Stroma

  21. Microscopy workflow 1 Figure 10: Confocal scanning workflow

  22. Microscopy workflow 1 Figure 11: Cancer image stack on Optiportal

  23. Microscopy workflow 2 Figure 12: Therapy effectiveness measurement workflow

  24. Microscopy workflow 2 Figure 13: Therapy effectiveness calculation on Optiportal

  25. Conclusions & future works • SWF-TDW linkage • Demonstration the system with a case study in optical microscopy • To-dos • Support more data-types (currently images and movies) • Support other middleware • Support more interactive modes of operation: computational steering environment.

  26. Thank you for listening! Questions are welcome!

  27. References • [1] Lin, C., Lu, S., Lai, Z., Chebotko, A., Fei, X., Hua, J. and Farsha, F. “Service-oriented architecture for view: A visual scientific workflow management system.”, In SCC ’08: Proceedings of the 2008 IEEE International Conference on Services Computing, pages 335–342, Washington, DC, USA, 2008. IEEE Computer Society. • [2] https://kepler-project.org/users/copy_of_LotkaWorkflow.png/image_large • [3] http://systems.cs.princeton.edu/omnimedia/images/back24.jpg • [4] http://messagelab.monash.edu.au/Infrastructure/OptiPortal • [5] http://www.sagecommons.org/images/stories/SAGEcomponents.jpg

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