1. Cancer Bioinformatics Grid (caBIG) CANS 2006 Chicago, Illinois
Shannon Hastings Department of Biomedical Informatics Ohio State University

2. National Cancer Institute 2015 Goal
Relieve suffering and death due to cancer by the year 2015

3. Cancer Biomedical Informatics Grid (caBIGTM)
The cancer Biomedical Informatics Grid (caBIG™), is a voluntary network or grid connecting individuals and institutions to enable the sharing of data and tools, creating a World Wide Web of cancer research. The goal is to speed the delivery of innovative approaches for the prevention and treatment of cancer. The infrastructure and tools created by caBIG™ also have broad utility outside the cancer community.
National Cancer Institute Initiative
Over 800 Participants
Over 80 Organizations
Over 70 Projects

4. Origins of caBIG
Need: Enable investigators and research teams nationwide to combine and leverage their findings and expertise in order to meet NCI 2015 Goal.
Strategy: Create scalable, actively managed organization that will connect members of the NCI-supported cancer enterprise by building a biomedical informatics network

5. caBIG Community Organization

6. caBIG Overview
Common, widely distributed infrastructure that permits the cancer research community to focus on innovation
Shared, harmonized set of terminology, data elements, and data models that facilitate information exchange
Collection of interoperable applications developed to common standards
Cancer research data is available for mining and integration

7. Semantic interoperability
The ability of multiple systems to exchange information and to be able
to use the information that has been exchanged.
Semantic interoperability
Syntactic interoperability

8. caBIG Compatibility Guidelines
SYNTACTIC
SEMANTIC
caBIG Compatibility Guidelines

9. Gold compliance creates the G in caBIG
What is caGrid?
Development project of Architecture Workspace, aimed at helping define and implement Gold Compliance (the highest level of caBIG compatibility)
Gold compliance creates the G in caBIG
Gold => Grid => connecting Silver Compliant Systems
No requirements on implementation technology is necessary for Gold compliance
Specifications will be created defining requirements for interoperability
caGrid provides core infrastructure, and tooling to provide “a way” to achieve Gold compliance

10. caGrid Conceptual View
Microarray
NCICB
Research
Center
Gene
Database
Grid-Enabled Client
Tool 1
Tool 2
caArray
Protein Database
Tool 3
Tool 4
Grid Data Service
Analytical Service
Image
Grid Services Infrastructure
(Metadata, Registry, Query,
Invocation, Security, etc.)
Grid Portal

11. caGrid Data Description Infrastructure
Client and service APIs are object oriented, and operate over well-defined and curated data types
Objects are defined in UML and converted into ISO/IEC Administered Components, which are in turn registered in the Cancer Data Standards Repository (caDSR)
Object definitions draw from vocabulary registered in the Enterprise Vocabulary Services (EVS), and their relationships are thus semantically described
XML serialization of objects adhere to XML schemas registered in the Global Model Exchange (GME)

12. Conceptual View of the Problem

13. caGrid Components Leverage existing technologies:
caDSR, EVS, Mobius GME: Common data elements, controlled vocabularies, schema management
Globus Toolkit (currently version 4.0.3)
Core grid services infrastructure
Service deployment, service registry, invocation, base security infrastructure
Additional Core Infrastructure
Higher-level security services (Dorian, GTS, GridGrouper)
Grid service access to metadata components (caDSR, GME, etc)
Workflow, Identifier services
Service Provider Tooling (Introduce)
Graphical service development and configuration environment
Abstractions from service infrastructure for Data and Analytical services
Deployment wizards
Client Tooling
High-level APIs for interacting with core components and services
Graphical Tools

14. Grid Authentication and Authorization with Reliably Distributed Services (GAARDS)
The GAARDS Security Infrastructure provides services and tools for the administration and enforcement of security policy in an enterprise Grid.
Developed on top of the Globus Toolkit
Extends the Grid Security Infrastructure (GSI)
Provide enterprise services and administrative tools for:
Grid User Management
Identity Federation
Trust management
Group/VO management
Access Control Policy management and enforcement
Integration between existing security domains and the grid security domain.
Security Infrastructure for the Cancer Biomedical Informatics Grid (caBIGTM)

15. GAARDS Services Dorian Grid Trust Service (GTS) Grid Grouper
Grid User Account Management
Integration point between external security domains and the grid.
Allows accounts managed in external domains to be federated and managed in the grid.
Dorian allows users to use their existing credentials (external to the grid) to authenticate to the grid
Grid Trust Service (GTS)
Creation and Management of a federated trust fabric.
Supports applications and services in deciding whether or not signers of digital credentials/user attributes can be trusted.
Supports the provisioning of trusted certificate authorities and corresponding CRLS.
Grid Grouper
Group management service for the grid
Provides a group-based authorization solution for the Grid
Enforce authorization policy based on membership to groups

16. Accessing caGrid workflow
Data Service
@ uchicago.edu
BPEL
Workflow
Doc
Workflow
inputs
Workflow
Mgmt
Service
BPEL
Engine
Analytic service
@ duke.edu
Workflow
Results
Analytic service
@ osu.edu
Workflow management service
Sharing workflows
Get workflow status

17. Introduce Graphical Development Environment (GDE)
GUI for creating and manipulating a grid service
Provides means of simple creation of service skeleton that a developer can then implement, build, and deploy
Automatic code generation of complete caBIG compliant grid service which is configured to provide:
Security
Advertisement
Discovery
Complete Client API
Provides a set of tools which enable the developer to add/remove/modify/import methods of the service as well create sub-services.
Automatic code generation of all the required code, Globus grid service code/configuration, service configuration, implementation of the client, and stubbed implementation of the service

18. Introduce Generated Grid Service Architecture
Base service is a GT4 based WSRF capable grid service.
Utilize compositional inheritance (in lieu of non-standard port type extensions) to enable the service to inherit required features such as providing service security metadata and access to resource properties.
Utilize JNDI for server side configuration properties, and resources and resource properties.
Provide client and service side wrappers which implement the service designers interface as opposed to the document literal interface generated by Axis.
Provide metadata registration to the index service by configuring the Resource to register it’s service groups to a predefined caGrid MDS based Index Service.

19. Collaborating Architects and Developers
Ohio State University
Argonne National Lab
Duke University
Georgetown University
Semantic Bits

20. Project Resources and Communication
caBIG at NCI
Globus Dev
caGrid 1.0 GForge Home:
Feature Requests
Bug Reports
Discussion Forums
Public Wiki
Quality Dasboards
Downloads / Source Repository
caGrid Users Mailing List

21. Cancer Bioinformatics Grid (caBIG) CANS 2006 Chicago, Illinois
Shannon Hastings Department of Biomedical Informatics Ohio State University