kisti e-science workbench
DESCRIPTION
KISTI e-Science workbench. 2008. 9. 9. Dongsoo Han, 1 Soonwook Hwang 2 1 Information and Comunication University 119 Munjiro, Yuseong-Gu, Daejeon, Korea 2 Korea Institute of Science and Technology Information 335 Gwahangno, Yuseong-gu, Daejeon, Korea [email protected], [email protected]. - PowerPoint PPT PresentationTRANSCRIPT
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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
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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!