David Abramson &Hoang Anh Nguyen

Monash University

Background◦ Scientific Workflow◦ Tiled Display Wall◦ Why do we need a SWF-TDW link ?

Design and Implementation Case Study Conclusions & Future works

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.

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

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

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

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

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

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

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

Figure 4: SAGE architecture

SAIL: Sage Application Interface Library

Sagereceiv

er

Sagereceiv

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Sagereceiv

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Sagereceiv

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FreeSpace

Manager

FreeSpace

Manager

UI Client

UI Client

UI Client

UI Client

SAILSAIL

App 1App 1

SAILSAIL

App 2App 2 App 3App 3

SAILSAIL

SAGE messages

Pixel stream

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

Goals:◦ Provide seamless link between SWFs and TDW◦ Middleware independence◦ Future user interactions

Design Alternatives◦ SSH actor◦ SAGE actor◦ Distributed architecture: dedicated server

SSH

pro

toco

lSSH

pro

toco

l Simple Inflexible

Simple Inflexible

SSH ActorSSH Actor

Figure 5: Solution using SSH actor

messages

Pixel stream

Sagereceive

r

Sagereceive

r

Sagereceive

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Sagereceive

r

Sagereceiver

Sagereceiver

FreeSpaceManag

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UI Client

UI Client

App App

SAILSAIL

SAGE actor

UI Client

UI Client

JNIJNIKepler code (Java)

Kepler code (Java)

SAILSAIL SAILSAIL

Figure 6: SAGE actor block diagram

compact possible feeding user feedbacks to workflow intensive computation on machine running Kepler middleware dependent

compact possible feeding user feedbacks to workflow intensive computation on machine running Kepler middleware dependent

Figure 7: Distributed Architecture

Server Interface

Server Interface

OptIPortalMiddlewar

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OptIPortalMiddlewar

eServer

Interface

Server Interface

Server Interface

Server Interface

OptiServerOptiServer

OptIPortal

Kepler

OptIPortal Actor

OptIPortal Actor

OptIPortalMiddlewar

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OptIPortalMiddlewar

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OptIPortalMiddlewar

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OptIPortalMiddlewar

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middleware-independent highly distributed small communication overhead

middleware-independent highly distributed small communication overhead

Figure 8: Implementation

messages

Pixel stream

Sagereceiver

Sagereceiver

Sagereceiver

Sagereceiver

Sagereceiver

Sagereceiver

FreeSpaceManag

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FreeSpaceManag

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SAILSAIL

App 1

App 1

SAILSAIL

App 2

App 2

App 3

App 3

SAILSAIL

OptiUI Client

OptiUI Client

OptiServerOptiServer

Kepler OptIPortal Actor

OptIPortal Actor

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

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

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

Nuclei

Stroma

Blood vessels

Merged image

Figure 10: Confocal scanning workflow

Figure 11: Cancer image stack on Optiportal

Figure 12: Therapy effectiveness measurement workflow

Figure 13: Therapy effectiveness calculation on Optiportal

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.

[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