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KISTI e-Science workbench

2008. 9. 9

Samsung-ICU E-Health Research Center

Dongsoo Han,1 Soonwook Hwang2

1Information and Comunication University119 Munjiro, Yuseong-Gu, Daejeon, Korea

2Korea Institute of Science and Technology Information335 Gwahangno, Yuseong-gu, Daejeon, Korea

dshan@icu.ac.kr, hwang@kisti.re.kr

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Introduction

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The GRID infrastructure matures, and remote devices such as sensors and electron microscopes that can be handled through the internet proliferates

Scientists usually have no sufficient programming skills to integrate available services

GRID toolkits is not successful for supporting general scientists who are not familiar with programming

Need a new e-Science working environment

Backgrounds

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How can we put all the resources together so that researchers can easily access the resources to accomplish their research goals?

Provide the resources in a form of easily accessible services and provide tools to find and integrate such services

General Issues in e-Science

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Workflow system is often used for the service integration

Web services technology is quite useful for preparing and announcing services

But the answer is still yes and no because…

Currently available tools and technologies are not enough ?

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Service users often develop own services by themselves Should be flexible in integration and development Usually takes try and error approaches

Handles not only structured data but also semi-structured or unstructured data Often processes raw files and data Thus filters, converters, auxiliary functions and facilities such

as parsers often need to be developed in the process

Involves huge data and high cost devices or computing resources

Recovery is usually not a big concern

e-Science Service Characteristics(1/2)

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Focused more on the development of service process rather than the service process automation

Eg) Taverna Project, U-health service process development

Incorporation of GRID infrastructure and resources in service process

Thus the key features of e-Science workflow should come out from the support of the service development process in GRID environment need to understand the development process of each domain sometimes collaboration support is essential

e-Science Service Characteristics(2/2)

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developing stagerunning stage

feed back

business workflow

science workflow

Business Workflow vs Science Workflow

area to focus

design, validation, simulation, running, monitoring

Modeling/Design, validation, simulation, running, monitoring?

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e-Science Workbench

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Software system that helps scientists design and automate their e-Science experiments on the GRID or internet environments without the support of programmers.

Equipped with a way of richer facilities than conventional GRID toolkits

Need mechanisms or structures to accommodate diverse e-Science requirements - Layered architecture, Incremental approach

e-Science Workbench

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e-Science workbench is usually positioned on the top of GRID workflow system that supports ad hoc workflow

Workflow or workflow system is domain neutral, whereas e-Science workbench is better to be domain specificBio workbench, Health workbench, e-Airs workbench, ..

Workbench should provide not only process modeling tool but also domain specific process development process and associated facilitiesHealth service vs health service development process

Unlike workflow system, e-Science workbench should provide interfaces for process modeling, execution, monitoring/administration, and modification in integrated manner

Workflow vs Workbench

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Supports multi-grid platformsgLite, Globus Toolkit

Separates common and specific parts of application domains for the efficient construction of workbench for each domainCommon part: Ontology, Web services incorporationSpecific part: Parametrization, Analysis methods, …

Supports service development process for each domain

Based on flexible GRID workflow system that supports ad hoc workflow

Provides a unique means for the flexible and centralized control of distributed and autonomous resources Ubiscripts

KISTI e-Science Workbench

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Globus gLite

GRID workflow(WebVine)

e-Science Workbench Common Platform

Ub

script

e-Airsworkbench

Life/Healthworkbench

Bioworkbench

KISTI e-Science Workbench

Applications

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Workflow system adopted for KISTI e-Science workbench

Provides easy ways to access Globus or gLite toolkit and supports ad hoc workflow

Incorporates web services and ontology technologies

Light workflow management systemNo transaction supportMay not have a recovery mechanismMay not have an exception handling mechanism

WebVine Workflow Management System

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Placed on the top of workflow system and contains common modules for e-Science workbenches

Integrates user interfaces of workflow system

Includes modules to support ontologies and other modules for the support of advanced features

e-Science Workbench Common Platform

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Globus gLite

GRID workflow(WebVine)

Ub

script

e-Airsworkbench

Life/Healthworkbench

Bioworkbench

e-Science Workbench Platform

• Ontology Based BPMT• Runtime Client• Admin/Monitoring Tool

• Ontology Editor• Service Broker• Service Recommendation

• Service Registration• Service Repository

e-Science Workbench Common Platform

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Bio-Workbench

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The first domain specific workbench developed on

our e-Science workbench

Supports biologists who want to find valuable information by integrating bioinformatics Web services

Bio-pipe enables biologists to search and choose available Web services, and integrate the chosen Web services for the final results

Bio-Pipe

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내부사용자

업무담당자

시스템관리자

BioPortal BioEngineBioEngine

시시스스템템관관리리//모모니니터터링링

BioManager

• 유전체 조회• 발현체 조회• 질환체 조회

통합게놈뷰어

• 자료의 관리• FTP 자료서비스

파일 /FTP 관리

대국민

일반국민

유관단체

전문가

생생명명정정보보

포포탈탈

Bio Workbench

• 프로젝트관리• 프로젝트

Packing/Unpacking

• 프로젝트 DB• 모듈디자인 및 관리• 모듈 온톨로지• 모듈 Import/Export

• 문서작성• 게시판• WIKI• 모니터링• 프로그램관리• 회원관리• 관리자메일링서비스 • 스카마관리

• 데이터의 조회

데이터베이스관리

• 서버상태조회• 이용자현황조회

웹서버관리

• 리소스사용 , 활성화 조회• 네트워크 부하

모니터링관리BioCellBioBody

WorkFlow

유전체DB

단백질체DB

발현체DB

질환체DB

문헌정보DB

신약물DB

DB 백업서버

유관시스템 연계

• 해부학적 온톨로지 기반분류 및 시각화

• 질병학적 온톨로지 기반분류 및 시각화

인체 구조 기반의정보분석

• 단백질상호작용 표현• 대사 , 신호전달경로 표현

세포구조 기반의데이터 가시화

생명정보 시각화 정보

추출기

생명정보 데이터 통합기

생명정보 색인

처리기

생명정보 지식

추출기

생명정보 웹 어플리케이션 서버

생명정보 웹 어플리케이션 서버

한국정보문화진흥원

국가지식포털시스템

한국정보문화진흥원

국가지식포털시스템과학기술분야

종합정보시스템과학기술분야

종합정보시스템

외부연계 시스템

국가지식정보포털

The Big Picture of Bio Workbench

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e-Science Workbench Platform

A web site for Bio-Pipe contest: a hundred of bio-pipes are successfully submitted and deployed on the siteA web site for Bio-Pipe contest: a hundred of bio-pipes are successfully submitted and deployed on the site

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Bio-Workbench Demo

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U-Health Workbench

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U-health workbench aims to support doctors or medical experts in designing and delivering their proprietary u-health services to users

Assumptions– U-Health service requires various personalized services– The users of the workbenches are not programmers but

doctors who have no skills in programming

Deals with various components such as bio-sensors,

gateways, cellular phones, and service modules to

support the construction of service scenarios

U-Health Workbench

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Web Servicesu-Health Service

Registry

u-Health ProcessAsset Library

t3 t4t2

Validation CheckUser Registration

Check Bio Data Type

Health ProgramAnalysis

Store Data

+

t1

Start

+t5

u-Health Process

store

retrieve

register

discover

XML messages (SMM, SQM, …)

Serv

ice

Leve

lPr

oces

s Le

vel

App

licat

ion

Leve

l

ProcessDesigner

WebVineBPM Engine

execute

edit

Service Developer

develop/register

MobileApplications

WebApplications(Web Portal)

STRESS OBESITY DEPRESSION DIABETES ETC…

Architecture of U-Health Workbench

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U-Health 워크벤치 도구U-Health Workbench Snapshot

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Diagnosis Framework (DCAP)

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User Interfaces

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U-Health Workbench Demo

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Workflow based service integration and enactment

Ontology based inference and service construction

Integration of distributed DBs and devices

Portal service incorporation

Supports not programmers but domain experts in designing and running their services

Commonly Used Technologies

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We developed an e-Science workbench on the GRID environment

Two domain-specific workbenches are successfully developed on e-Science workbench common platform

The three-layer structure of e-Science workbench was revealed useful in systematically stacking modules for building the entire e-Science workbench

In order to announce the e-Science workbench to the public, more functions and modules must be prepared and more domain-specific e-Science workbenches should be developed in the e-Science workbench.

Summary

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Thank you!