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Cancer Bioinformatics Grid (caBIG) CANS 2006 Chicago, Illinois. Shannon Hastings [email protected] Department of Biomedical Informatics Ohio State University. National Cancer Institute 2015 Goal. Relieve suffering and death due to cancer by the year 2015.

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Cancer bioinformatics grid cabig cans 2006 chicago illinois l.jpg

Cancer Bioinformatics Grid (caBIG)CANS 2006Chicago, Illinois

Shannon [email protected] of Biomedical InformaticsOhio State University

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National Cancer Institute 2015 Goal

Relieve suffering and death due to cancer by the year 2015

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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

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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

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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

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  • The ability of multiple systems to exchange information and to be able

    to use the information that has been exchanged.


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caBIG Compatibility Guidelines

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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

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Grid-Enabled Client

Analytical Service



Tool 1


Tool 2




Protein Database

Grid Services Infrastructure

(Metadata, Registry, Query,

Invocation, Security, etc.)

Grid Data Service

Tool 3

Tool 4

Grid Portal





Tool 2

Tool 3

caGrid Conceptual View

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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 11179 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)

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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

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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)

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GAARDS Services

  • Dorian

    • 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

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Data Service


Accessing caGrid workflow











Analytic service




Analytic service


  • Workflow management service

    • Sharing workflows

    • Get workflow status

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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

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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.

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Collaborating Architects and Developers

  • Ohio State University

  • Argonne National Lab

  • Duke University

  • Georgetown University

  • Semantic Bits

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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


    • [email protected]

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Cancer Bioinformatics Grid (caBIG)CANS 2006Chicago, Illinois

Shannon [email protected] of Biomedical InformaticsOhio State University