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KISTI e-Science workbench

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

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KISTI e-Science workbench

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  1. KISTI e-Science workbench 2008. 9. 9 Dongsoo Han,1 Soonwook Hwang2 1Information and Comunication University 119 Munjiro, Yuseong-Gu, Daejeon, Korea 2Korea Institute of Science and Technology Information 335 Gwahangno, Yuseong-gu, Daejeon, Korea dshan@icu.ac.kr, hwang@kisti.re.kr Samsung-ICU E-Health Research Center

  2. Introduction

  3. Backgrounds • 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

  4. General Issues in e-Science • 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

  5. Currently available tools and technologies are not enough ? • 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…

  6. e-Science Service Characteristics(1/2) • 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

  7. e-Science Service Characteristics(2/2) • 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

  8. Business Workflow vs Science Workflow business workflow feed back design, validation, simulation, running, monitoring science workflow area to focus Modeling/Design,validation, simulation, running, monitoring? developing stage running stage

  9. e-Science Workbench

  10. e-Science Workbench • 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

  11. Workflow vs Workbench • 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 specific • Bio workbench, Health workbench, e-Airs workbench, .. • Workbench should provide not only process modeling tool but also domain specific process development process and associated facilities • Health 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

  12. KISTI e-Science Workbench • Supports multi-grid platforms • gLite, Globus Toolkit • Separates common and specific parts of application domains for the efficient construction of workbench for each domain • Common part: Ontology, Web services incorporation • Specific 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

  13. KISTI e-Science Workbench e-Airs workbench Life/Health workbench Bio workbench Applications e-Science Workbench Common Platform GRID workflow(WebVine) Ubscript Globus gLite

  14. WebVine Workflow Management System • 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 system • No transaction support • May not have a recovery mechanism • May not have an exception handling mechanism

  15. e-Science Workbench Common Platform • 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

  16. e-Science Workbench Platform e-Airs workbench Life/Health workbench Bio workbench • Ontology Based BPMT • Runtime Client • Admin/Monitoring Tool • Ontology Editor • Service Broker • Service Recommendation • Service Registration • Service Repository e-Science Workbench Common Platform GRID workflow(WebVine) Ubscript Globus gLite

  17. Bio-Workbench

  18. Bio-Pipe • 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

  19. 일반국민 외부연계 시스템 대국민 내부사용자 시스템관리/모니터링 생명정보 포탈 모니터링관리 파일/FTP관리 통합게놈뷰어 데이터베이스관리 웹서버관리 Bio Workbench 유관단체 • 유전체 조회 • 발현체 조회 • 질환체 조회 • 프로젝트관리 • 프로젝트 Packing/Unpacking • 프로젝트 DB • 모듈디자인 및 관리 • 모듈 온톨로지 • 모듈 Import/Export • 문서작성 • 게시판 • WIKI • 모니터링 • 프로그램관리 • 회원관리 • 관리자메일링서비스 • 스카마관리 • 데이터의 조회 • 서버상태조회 • 이용자현황조회 • 자료의 관리 • FTP 자료서비스 • 리소스사용, 활성화 조회 • 네트워크 부하 전문가 한국정보문화진흥원국가지식포털시스템 과학기술분야종합정보시스템 DB백업서버 The Big Picture of Bio Workbench BioManager BioEngine BioPortal 업무 담당자 유관시스템 연계 WorkFlow 생명정보 웹 어플리케이션 서버 BioCell BioBody 생명정보 데이터 통합기 세포구조 기반의 데이터 가시화 인체 구조 기반의 정보분석 시스템 관리자 생명정보 시각화 정보 추출기 생명정보 색인 처리기 생명정보 지식 추출기 • 단백질상호작용 표현 • 대사, 신호전달경로 표현 • 해부학적 온톨로지 기반분류 및 시각화 • 질병학적 온톨로지 기반분류 및 시각화 국가지식정보포털 유전체 DB 단백질체 DB 발현체 DB 질환체 DB 문헌정보 DB 신약물 DB

  20. e-Science Workbench Platform A web site for Bio-Pipe contest: a hundred of bio-pipes are successfully submitted and deployed on the site

  21. Bio-Workbench Demo

  22. U-Health Workbench

  23. U-Health Workbench • 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

  24. Architecture of U-Health Workbench Application Level STRESS OBESITY DEPRESSION DIABETES ETC… Web Applications (Web Portal) Mobile Applications edit Process Level store execute retrieve u-Health Process u-Health Process Asset Library Process Designer WebVine BPM Engine XML messages (SMM, SQM, …) Service Level + u-Health Service Registry t1 t5 Web Services + Start Health Program Analysis t2 t3 t4 register Check Bio Data Type Store Data Validation Check User Registration develop /register discover Service Developer

  25. U-Health Workbench Snapshot U-Health 워크벤치 도구

  26. Diagnosis Framework (DCAP)

  27. User Interfaces

  28. U-Health Workbench Demo

  29. Commonly Used Technologies • 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

  30. Summary • 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.

  31. Thank you!

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