e-science workbench: an approach to build domain-specific problem solving environments

e-Science 2008 - 1Dongsoo Han, School of Engineering, ICU

e-Science workbench: an Approach to Build Domain-specific Problem

Solving Environments

2008. 12. 11

Samsung-ICU E-Health Research Center

Dongsoo Han1, Soonwook Hwang2

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

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

[email protected], [email protected]

Dongsoo Han, School of Engineering, ICU


Introduction


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 devices and services.

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

Need a new e-Science working environment.


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.

Currently available Workflow, Web services and GRID technologies are not enough to support the needs from specific domains.

General Issues in e-Science and Motivations


Develop domain-specific problem solving environments to facilitate the use of available services and resources for scientists to develop services and applications in their research domain.

Understand the characteristics and requirements of e-Science services and develop an e-Science workbench that satisfies such requirements.

In developing the e-Science workbench, adopt layered architecture so that we can use currently available technologies as long as possible.

Our approaches


Service users often develop their own services by themselves.Should be flexible in integration and developmentUsually 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 special purpose parsers often needed 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)


Focused more on the service process development 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 domainsometimes collaboration support is essential

e-Science Service Characteristics(2/2)


Business Workflow vs Science Workflow

developing stagerunning stage

feed back

business workflow

science workflow

area to focus

design, validation, simulation, running, monitoring

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


e-Science Workbench


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


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

Workflow system is domain neutral, whereas e-Science workbench is better to be domain specific.Bio workbench, U-health workbench, e-Airs workbench, ..

Workbench should be equipped with not only process modeling tool but also domain specific service development templates and associated facilities.Health service process vs health service development templates

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

Workflow vs Workbench


Supports multi-grid platformsgLite, Globus Toolkits

Separates common and specific parts of application domains for the efficient construction of workbench for each domainCommon part: Ontology, Web services incorporationSpecific part: Parameter sweeping, 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


KISTI e-Science Workbench

Globus gLite

GRID workflow(WebVine)

e-Science Workbench Common Platform

Ub

script

e-Airsworkbench

Life/Healthworkbench

Bioworkbench

Applications


Workflow system adopted for KISTI e-Science workbench.

Provides facilities 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


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 Platform

Globus gLite

GRID workflow(WebVine)

Ub

script

e-Airsworkbench

Life/Healthworkbench

Bioworkbench

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

• Ontology Editor• Service Broker• Service Recommendation

• Service Registration• Service Repository



Bio-Workbench


Process TemplateProcess Template

Service Pool

A Sub-processA Sub-process

ServiceBrokerServiceBroker

ProcessManagerProcessManager

Application Developers

Service Developers

Service Development

Tool

Service Development

Tool

Ontology and Process Modeling


Bio-Workbench


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


InternalUser

Participant

Administrator

BioPortal Bio WorkbenchBio Workbench

AAddmmiinn//MMoonniittoorriinngg

BioManager

• Genome viewer• Phenome viewer• SNP viewer

Genome Viewer

• 자료의 관리• FTP 자료서비스

File/FTP mgm.

Users

Biologists

Research Institutes

GeneralUsers

PPoorrttaall

• Project creation• Bio-pipe design• Service ontology• Service import/export

• Document• Board• WIKI• Monitoring• Program• User • Mail

• 스카마관리• 데이터의 조회

DB mgm.

• 서버상태조회• 이용자현황조회

Web server mgm.

• 리소스사용 ,• 활성화 조회• 네트워크 부하

MonitoringBioCellBioBody

WorkFlow

GenomeDB

ProteomeDB

PhenomeDB

SNPDB

LibraryDB

DrugDB

DB Servers

Interoperaton

• 해부학적 온톨로지 기반분류 및 시각화

• 질병학적 온톨로지 기반분류 및 시각화

Human Body Info.

• 단백질상호작용 표현• 대사 , 신호전달경로 표현

Cell Data생명정보 시각화 정보

추출기

Search Engine

생명정보 색인

처리기

생명정보 지식

추출기

Bioinformatics Web Server

Bioinformatics Web Server

KADO PortalKADO Portal

Science-TechnologyIntegration

Science-TechnologyIntegration

External Systems

National Knowledge

Portal

Bio Workbench and Surrounding Components

E-Science Workbench


e-Science Workbench Platform

A web site for Bio-Pipe contest: a hundred of bio-pipes are successfully submitted and deployed at http://biocommunity.kr.A web site for Bio-Pipe contest: a hundred of bio-pipes are successfully submitted and deployed at http://biocommunity.kr.


Bio-Workbench Demo


U-Health Workbench


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

Deals with various components such as bio-sensors,

gateways, cellular phones, and service modules to

support the construction of service scenarios.

Implemented on our e-Science workbench.

Assumptions

– U-Health service requires various personalized services

– The users of the workbenches are not programmers but

doctors who have no skills in programming

U-Health Workbench


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


U-Health Application Model

The U-health workbench provides a guideline based on a u-health application model.

The guideline is implemented in a form of a process template.

U-health application model


U-Health 워크벤치 도구An Application on U-Health Workbench


Diagnosis Framework (DCAP)


User Interfaces


U-Health Workbench Demo


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


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


Thank you!

e-science workbench: an approach to build domain-specific problem solving environments

Documents