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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

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

David Abramson &

Hoang Anh Nguyen

Monash University

outline
Outline
  • Background
    • Scientific Workflow
    • Tiled Display Wall
    • Why do we need a SWF-TDW link ?
  • Design and Implementation
  • Case Study
  • Conclusions & Future works
scientific workflow swf
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.
scientific workflow swf4
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
kepler swfms
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
kepler swf
Kepler SWF

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

tiled display wall tdw
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
tiled display wall tdw8
Tiled Display Wall (TDW)

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

tiled display wall tdw9
Tiled Display Wall (TDW)

Figure 3: An Optiportal at Monash Clayton ( Source [4] )‏

optiportal tdw
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
slide11
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

why do we need a tdw swf link
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
design
Design
  • Goals:
    • Provide seamless link between SWFs and TDW
    • Middleware independence
    • Future user interactions
  • Design Alternatives
    • SSH actor
    • SAGE actor
    • Distributed architecture: dedicated server
ssh actor
SSH actor
  • Simple
  • Inflexible

SSH protocol

SSH Actor

Figure 5: Solution using SSH actor

sage actor

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

dedicated server
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

prototype implementation
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

case study
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
antibody cancer therapies
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
antibody cancer therapies20
Antibody cancer therapies*

Nuclei

Blood vessels

Figure 9: Cancer Nuclei, Blood vessels, Stroma in confocal microscopy

Merged image

Stroma

microscopy workflow 1
Microscopy workflow 1

Figure 10: Confocal scanning workflow

microscopy workflow 122
Microscopy workflow 1

Figure 11: Cancer image stack on Optiportal

microscopy workflow 2
Microscopy workflow 2

Figure 12: Therapy effectiveness measurement workflow

microscopy workflow 224
Microscopy workflow 2

Figure 13: Therapy effectiveness calculation on Optiportal

conclusions future works
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.
references
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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