NCSU-1 V1/26-Mar-02 1

Context-sensitive Service Composition for Support of

Scientific Workflows

Mladen A. Vouk

North Carolina State University, Raleigh, NC

NCSU-2 V1/26-Mar-02 2

TeamSystem Engineering and Software• Prof. Mladen Vouk (scientific workflows, middleware, networks)• Sandeep Chandra, MS candidate (system, middleware)• Zhengang Cheng, PhD candidate (agents, protocols, services,

workflows)• Prof. Munindar Singh (agents, workflows, data-bases)Domain-Specific Workflows• Prof. Donald Bitzer (signal analysis, coding theory)• E. Eni-May, PhD candidate (bioinformatics, coding-theory)• Dr. David Rosnick (bioinformatics, entropy analysis)• Prof. Anne Stomp (genetic engineering)Coordination (Dr. T. Critchlow + others)• Dr. Tom Potok (project coordination, software)• Other ORNL project scientists

NCSU-3 V1/26-Mar-02 3

Philosophy?• Human-centric workflow support (appliance-

like) – case study Bioinformatics• Service-oriented (distributed and diverse data

access, storage, manipulation, analysis, and display, grid-based computing, end-user profile services, quality of service)

• Context-sensitive (end-user presence, location, expertise, access and interaction permissions, domain translation, p2p communications, etc.)

NCSU-4 V1/26-Mar-02 4

(In)efficient

End-User

Apps

Data and Compute

Communications

OS

NCSU-5 V1/26-Mar-02 5

Example Workflow – Top LevelInput (select, slice and dice data):

– Obtain 3' end 16/18S ribosome for selected organism– Obtain sequences of mature mRNA for organism (or DNA if unavailable)

Process (model, compare, display, etc.):– Compute free energy bindings between 3' end of 16/18S rRNA and

mRNA– Train decision mechanism based on subset of mRNA sequences– Perform signal analysis on remaining (or newly requested) binding

sequences to determine efficiency

Output and analyze efficiency/signal model/data– Review results and compare to published efficiency/frameshift data (e.g.,

Nucleic Acids Research, J. Molecular Biology)– Evaluate theory in light of information theory (Shannon, Schnieder

NCSU-6 V1/26-Mar-02 6

How?• Domain-adequate computer-human interfaces

– Personalizing context/knowledge gateways

– Domain-aware workflow construction (service discovery, composition, invocation, agents, protocols)

• Adequate and seamless services, service registration and exchange gateways (move away from bring/cook-your-own service approach).

• Adaptive (policy-based) quality of service control and management all along the “service stack.”

NCSU-7 V1/26-Mar-02 7

Architecture

PARTICIPANT A

PARTICIPANT B

PARTICIPANT C

GENES

PHY’S

BIO

UDDI

HUMANCLIENT

WORKFLOW COMPOSITION &INTERFACES AGENT

SERVICE

AGENTSERVICE

AGENTSERVICE

All participants register their services

Directly connect touddi registry

Service & ContextGateways and Multiplexers

e.g., Iflow, JavaAgent

e.g., UDDI, NCBioGrid, WLS, IPPhones, H323Video

Vipar GenBank,BioNews

NCSU-8 V1/26-Mar-02 8

NCSU-9 V1/26-Mar-02 9

NCSU-10 V1/26-Mar-02 10

Service Agent - Example

DESCISIONMODULE

MESSAGINGSYSTEM

POLICY Remote

APP’S

OBJECT

INCOMING MESSAGES

WSDL and/orASDL method, access, behaviorPublishing(e.g., in UDDI)

SOAPInterface

Site specific

Human and agents should be able to consume published services. Workflow and pipeline are ways to consume services

NCSU-11 V1/26-Mar-02 11

What is a Service?• A service is an entity that can receive service request

and respond/deliver within a time, cost, reliability, security, etc., frame acceptable to the end-user. The service may be presented in the form of an intelligent agent, or simply as a servlet.

• The service provides access to its data, methods, and tools, etc., which usually is the property of a particular organization.

• In the original "Data Integration Architecture", the CM Wrapper and XML Wrapper represent a service, and provide services to other services. Here they are viewed as independent services that possess Intelligence.

NCSU-12 V1/26-Mar-02 12

Composition

AS1:S1

AS1:S2

AS2:S1

AS3:S2

WORKFLOW

AS1:S1 AS2:S1 AS2:S2 AS3:S2

AS1 AS2 AS3

S1 S2 S1 S2 S1 S2

PIPELINE

PIPELINE AND WORKFLOW

Synch, AsynchDiffering timescales

NCSU-13 V1/26-Mar-02 13

UDDI AT SDM4

SDM Interface to construct userWorkflows.(prot—iFlow In progress)

Services registeredWith UDDI at sdm4.99-sdm category991- vipar news992- vipar genes993- Data Serv994- Analysis Serv

Menu to selectdata services

Menu to select analysis services

Menu to selectVipar services

Browser Browser

DB2Databaseon sdm4

Vipar serverFor news

Vipar serverFor bioinfo

WWW

Db2xml wrapper

Getting details

Details returned

Selected options arequeried to the UDDI

Populate menus with the service details

Connect to vipar using RMI

Service 1 Service n Service m

Description of availableservices at sdm4 UDDIusing WSDL, XML or HTML.

Invoke any of the registered services

Download To local system

Invoke services Invoke services

Invoke service

Current Framework

NCSU-14 V1/26-Mar-02 14

Support

• CVS is version control system for our developments. It is used to share data and software.

• Eclipse is a Java IDE from IBM, available from www.eclipse.org. It has seamless integration with CVS repository and provides an integrated debugging environment.

NCSU-15 V1/26-Mar-02 15

Intial Project Architecture and Prototypes

df

PDB

XMLWrapper

XMLWrapper

VIPAR

XMLWrapper

API

Integrationcomponent /KB-Mediator

(KBM)

QueryDispatch

andCollection(QDaC)

CMWrapper

CMWrapper

CMWrapper

Source / AgentMetaDataRegistry

XWRAPWrapperGenerator

XQuery (subsets e.g. Sel/Proj)

:Bio

XMLWrapper

ExternalProgram

XQuery interfaceSelect/project only

if invoked, pre-processes query parameters and post-processes results

NCSU-16 V1/26-Mar-02 16

Things to Do?

• Cast the amazing array of tools and software scientists use as services, catalogue it and define/improve interfaces, and ease – focus on What rather than How (from user perspective).

• Create context gateways that will coordinate domain-specific interactions and services and help in creation of efficient workflows.

• NCSU specific, we plan to have a fully working prototype in place in the next 6 month period.

• Suggestions?

NCSU-17 V1/26-Mar-02 17

NCSU-18 V1/26-Mar-02 18

Prototypes

VIPAR - GenBANK

VIPAR - GenNEWS

Other

GENES

News

BIO

UDDI

David,ChiChi

WORKFLOW COMPOSITION &INTERFACES AGENT

SERVICE

AGENTSERVICE

All participants register their services

Directly connect touddi registry

Service & ContextGateways and Multiplexers

UDDI, WLS, IP-phones, H323 VideoNC BioGrid

Iflow, JavaAgentEm