Context-sensitive Service Composition for Support of Scientific Workflows

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Context-sensitive Service Composition for Support
of Scientific Workflows

• Mladen A. Vouk
• North Carolina State University, Raleigh, NC

2
Team

• System 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

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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.)

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(In)efficient
End-User
Apps
OS
Communications
Data and Compute
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Example Workflow Top Level

• Input (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

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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.

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Architecture
e.g., UDDI, NCBioGrid, WLS, IPPhones, H323Video
Service Context Gateways and Multiplexers
All participants register their services

UDDI
e.g., Iflow, JavaAgent
PARTICIPANT A
WORKFLOW COMPOSITION INTERFACES
AGENT SERVICE
GENES
PARTICIPANT B
Directly connect to uddi registry
AGENT SERVICE
PHYS
HUMAN CLIENT
PARTICIPANT C
AGENT SERVICE
BIO
Vipar GenBank,BioNews
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Service Agent - Example
SOAP Interface
DESCISION MODULE
MESSAGING
APPS
INCOMING MESSAGES
SYSTEM
Site specific
WSDL and/or ASDL method, access,
behavior Publishing (e.g., in UDDI)
Remote
POLICY
OBJECT
Human and agents should be able to consume
published services. Workflow and pipeline are
ways to consume services
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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.

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Composition
Synch, Asynch Differing time scales
AS1
AS2
AS3
S2
S1
S2
S1
S2
S1
AS1S1
AS2S1
AS2S2
AS3S2
PIPELINE
WORKFLOW
AS1S2
AS3S2
AS1S1
AS2S1
PIPELINE AND WORKFLOW
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Current Framework
WWW
Vipar server For news
Vipar server For bioinfo
UDDI AT SDM4
Getting details
Connect to vipar using RMI
Details returned
Populate menus with the service details
Services registered With UDDI at sdm4. 99-sdm
category 991- vipar news 992- vipar genes 993-
Data Serv 994- Analysis Serv
Selected options are queried to the UDDI
Menu to select data services
Menu to select analysis services
Menu to select Vipar services
Invoke services
Invoke services
SDM Interface to construct user Workflows. (prot
iFlow In progress)
Description of available services at sdm4
UDDI using WSDL, XML or HTML.
Browser
Browser
Db2xml wrapper
Invoke service
DB2 Database on sdm4
Invoke any of the registered services
Download To local system
Service 1
Service n
Service m
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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.

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Intial Project Architecture and Prototypes
if invoked, pre-processes query parameters and
post-processes results
Query Dispatch and Collection (QDaC)
XML Wrapper
XQuery (subsets e.g. Sel/Proj)

API
Bio
VIPAR
Integration component / KB-Mediator (KBM)
XML Wrapper
PDB
CM Wrapper
CM Wrapper
XML Wrapper
df
XML Wrapper
CM Wrapper
Source / Agent MetaData Registry
XQuery interface Select/project only
XWRAP Wrapper Generator
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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?

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Prototypes
UDDI, WLS, IP-phones, H323 Video NC BioGrid
Service Context Gateways and Multiplexers
All participants register their services
Iflow, JavaAgentEm

UDDI
VIPAR - GenBANK
WORKFLOW COMPOSITION INTERFACES
AGENT SERVICE
GENES
VIPAR - GenNEWS
Directly connect to uddi registry
AGENT SERVICE
News
David, ChiChi
Other
BIO