# Presentation: 587680

## caBIGTM Essentials: Self-Paced Training Program 

**Prepared by the caBIGTM Documentation and Training ****(D&T) Workspace –  Last Updated: 8 November 2007 **

***Getting Started: Click on right arrow below to advance to the next slide.***

## Training Topic, Audience & Prerequisites

**Topic Statement:  **This training provides an overview of the caBIGTM program and its offerings.  It introduces caBIGTM tools, describes different ways to connect with caBIGTM, and points to additional resources to support specific next steps. ** **
**Target Audience:**  This training program is designed for organizations wishing to learn about and then connect with caBIGTM. Specific audiences include leaders charged with planning and guiding caBIGTM deployment efforts in their organizations.
**Prerequisites:  **This training does not assume any pre-existing knowledge about caBIGTM.  Those familiar with caBIGTM may wish to skip material in Lesson 1, and proceed to later lessons.

**Training Overview:**

## Lesson Plan

**Lesson Plan**

- Lesson 1:  Introduction to caBIG
- Lesson 2:  caBIGTM Self-Assessment & Tools Overview
- Lesson 3:  Focus on Clinical Trials Compatibility Framework
- Lesson 4:  Focus on Life Sciences Distribution
- Lesson 5:  Making A Tool caBIGTM Compatible – Overview
- Lesson 6:  Focus on the Grid
- Lesson 7:  Focus on caBIGTM Data Sharing and Security Framework
- Lesson 8:  Conclusion

**Training Overview:**

## Training Program Goals

- By the end of this training, you will be able to:
- Describe the caBIGTM initiative and its goals.
- Locate caBIGTM software tools, so that you can evaluate their benefits against your needs, and determine their appropriateness for implementation in your organization’s environment.
- Explain the roles of interoperability, the Grid, and data sharing in achieving caBIGTM goals.
- Evaluate and select specific actions that your organization can take to connect with caBIGTM, including adopting caBIGTM tools and adapting your own tools to become caBIGTM compatible.

**Training Overview:**

## Overview of the Training Environment

## Lesson 1: Introduction to caBIGTM

**Lesson 1: Introduction to caBIGTM**

- This lesson introduces the purpose of caBIGTM and provides an overview of what it means to connect with caBIGTM.
- Learning Objectives for this Lesson:
- Describe caBIGTM and Its Goals
- Introduce the caBIGTM Structure and Organization
- Introduce Key caBIGTM Concepts
- Explain What it Means to Connect with caBIGTM
- Determine Your Path Forward
- Decide Where to Go Next in This Training

## caBIGTM and Its Goals 

- Launched in 2004, the cancer Biomedical Informatics Grid (caBIGTM) is an information technology program that is redefining how cancer research is conducted.
- The vision of caBIGTM is a full cycle of integrated cancer research, extending from bench to bedside, and back again.
- We do this by:
- Developing software tools that support cancer research efforts, and by
- Establishing a common infrastructure that can be used to share data and applications across organizations.

**Lesson 1: Introduction to caBIGTM **

## caBIGTM and Its Goals

**The Goals of caBIGTM are to: **** **
- Connect cancer research communities through a shareable and interoperable infrastructure
- Develop standard rules and a common language to more easily share information
- Build or adapt tools for collecting, analyzing, integrating, and disseminating information associated with cancer research

**Lesson 1: Introduction to caBIGTM **

*This training program is designed for people who want to support caBIGTM goals by adopting caBIGTM tools, applying the standards that support data sharing with others in the caBIGTM community, and connecting to the caBIGTM infrastructure.  If your interest in caBIGTM is more general, please visit the caBIGTM Public Website: *_[http://cabig.cancer.gov](http://cabig.cancer.gov/)__ –_*** Note: all links in this training open a new window/tab!***

## How Connecting with caBIGTM Benefits You

- Connecting with caBIGTM benefits cancer research organizations in the following ways:
- Facilitate collaborative research through greater access to research data made available through caBIGTM infrastructure.
- Increase the research potential from data sets, by facilitating the flow of data between multiple tools on the “bench to bedside” path.
- Install free customizable caBIGTM software applications to support the conduct of basic and clinical cancer research
- Learn about the tools and resources that other organizations are willing to share, and advertise your own presence and services to others.
***The increased data sharing made possible by connecting with caBIGTM increases the effectiveness and efficiency of cancer research, helping individual scientists, the cancer research community, and – ultimately - patients. ***

**Lesson 1: Introduction to caBIGTM **

## caBIGTM:  From Pilot to Enterprise

**2004 – **
**2006**

**caBIGTM:  From Pilot to Enterprise**

- caBIGTM began with the vision of creating a virtual web of interconnected data, individuals, and organizations that redefines how research is conducted, care is provided, and patients/participants interact with the research enterprise

**PILOT PHASE**
-   1,000 individuals from over 190 organizations
-   Developed a standards-based caGrid infrastructure
-   40 applications that support basic/ clinical cancer research

**ENTERPRISE PHASE**
-   Rollout of available caBIGTM tools and infrastructure to
-    NCI-designated Cancer Centers
-   Formation of an enterprise support network
-   Engagement with the broader biomedical research community

**2007**

**Lesson 1: Introduction to caBIGTM **

## caBIGTM Structure and Organization

- caBIGTM is sponsored by the National Cancer Institute (NCI), and is administered by the National Cancer Institute’s Center for Biomedical Informatics and Information Technology.
- Many caBIGTM activities are carried out in management structures called ***workspaces***.
- Domain workspaces focus on specific areas of cancer research, and oversee the development of domain-focused software tools.
- Cross-cutting and Strategic workspaces support these groups by developing standards, infrastructure, policies, and documentation.
- The following slides introduces these workspaces and their missions.

**Lesson 1: Introduction to caBIGTM **

## caBIGTM Organizational Overview

## caBIG Core Concepts

## What it Means to Connect with caBIGTM 

**There are two basic ways to become connected with caBIGTM: **** **
**Adopt a caBIGTM Tool and then Connect to the Grid: ** You can connect with caBIGTM by _adopting_ pre-existing caBIGTM compatible tools and then connecting through caGrid.  This is best if you need domain-specific tools, caBIGTM has tools that meet these needs, and you are prepared to install the caBIGTM tools and integrate them into your workflow.
**Adapt a Tool to make it caBIGTM Compatible and then Connect to the Grid:  **If you have a tool (either created in-house or by a vendor) that is not caBIGTM compatible, you can achieve compatibility by reengineering the existing tool or creating an interface that maps an existing tool’s data structures and APIs to caBIGTM standards.  Once the tool is compatible, you can connect to the Grid.
- The following sequence of diagrams shows how these options play out – ultimately aligning with the key concepts just covered.

**Lesson 1: Introduction to caBIGTM **

## Pathways to caBIGTM Compatibility

**caGrid**

**Pathways to caBIGTM Compatibility**

- App 1

**ADOPT**

- App 2

**ADAPT**

**Available caBIGTM         Applications**

**Lesson 1: Introduction to caBIGTM **

- There are many existing caBIGTM compatible applications that can be adopted and then connected to the Grid with ease.
- Lessons 2-4 introduce these tools.

## Pathways to caBIGTM Compatibility

- App 2

**caGrid**

**Pathways to caBIGTM Compatibility**

**ADOPT**

**ADAPT**

**Lesson 1: Introduction to caBIGTM **

- Connecting a caBIGTM compatible application to the Grid (creating a Grid node) is facilitated by caBIGTM tools and infrastructure – Lesson 6 addresses this process in more depth.

**Available caBIGTM         Applications**

## Pathways to caBIGTM Compatibility

- App 3

**caGrid**

**Pathways to caBIGTM Compatibility**

**ADAPT**

- App 1

**Existing **
**Applications**

**Available caBIGTM         Applications**

**ADOPT**

**ADAPT**

- App 2

**Lesson 1: Introduction to caBIGTM **

- You can also adapt your own tool to be caBIGTM compatible and then connect to the Grid – this is generally more labor intensive than adopting a tool, and will require support from a development team with certain skills and experience.  We discuss this in Lessons 5 and 6.

## Pathways to caBIGTM Compatibility

- App 3

**caGrid**

**Pathways to caBIGTM Compatibility**

**ADAPT**

- App 1

**ADOPT**

**ADAPT**

- App 2

**Lesson 1: Introduction to caBIGTM **

**Available caBIGTM         Applications**

**Existing **
**Applications**

- You do not need to make the entire application compatible to connect to the Grid – just the elements that you wish to expose.  Once compatibility is achieved, connecting to the Grid is facilitated by caBIGTM tools and infrastructure –
- Lessons 5 and 6 address these processes in more depth.

## Pathways to caBIGTM Compatibility

- App 3

**caGrid**

**Pathways to caBIGTM Compatibility**

**ADAPT**

- App 1

**ADOPT**

**ADAPT**

- App 2

**Lesson 1: Introduction to caBIGTM **

**Available caBIGTM         Applications**

**Existing **
**Applications**

## Life on the Grid: Implementation Scenarios

**Lesson 1: Introduction to caBIGTM **

## Determining the Best Path for You

**ADOPTING MAY BE BEST IF...**
- You have requirements that caBIGTM tools can fulfill in the domains of clinical trials, bench research, imaging, and/or tissue banking.
- End users are open to learning new tools and integrating them in their workflow.
- You do not have a technical team available to build or reengineer software, but you can to leverage internal resources to support a software installation effort.

**ADAPTING MAY BE BEST IF...**
- You have existing technology infrastructure and tools that meet the needs of the users, and that are already integrated into workflows.
- You have technical team(s) available with (1) software development expertise, particularly in the areas of data modeling and application programming interface (API) development. (2) Previous experience with the NCI’s vocabulary and data model tools/repositories.

- To learn about this path, you may want to focus on Lessons 2, 3 and 4

- To learn about this path, you may want to focus on Lessons 5 and 6

**Lesson 1: Introduction to caBIGTM **

## Determining the Best Path for You 

- While “adopt or adapt” are the two basic ways to connect with caBIGTM, hybrid approaches exist.  Here are two examples:
- Integrate a caBIGTM module within your existing bioinformatics infrastructure, and develop an interface to facilitate data exchange between them.
- Create a caBIGTM-compatible “wrapper” around an existing tool, so that data appropriate for external data sharing can be more easily served, while not reengineering an entire tool.
***Which options are best for your organization?  The rest of this training program will help you determine the best choices based on your existing needs, infrastructure, and capability.***

**Lesson 1: Introduction to caBIGTM **

## Decide Where to Go Next in This Training 

- Here’s some tips on what to explore **next** in this training:

**Lesson 1: Introduction to caBIGTM **

| If You Are Interested In... | Visit....  |
| --- | --- |
| Accessing a self-assessment and seeing the range of tools that caBIGTM has to offer. | Lesson 2:  caBIGTM Tools and Infrastructure Overview |
| Focusing on caBIGTM tools related to clinical trials management.  | Lesson 3:  Focus on the Clinical Trials Compatibility Framework |
| Learning more about caBIGTM tools related to bioinformatics research, bio-banking, and the Grid.  | Lesson 4:  Focus on Life Sciences Distribution
 |
| Determining whether your team is ready to engage in a development effort to adapt your existing tools to be caBIGTM compatible.   | Lesson 5:  Making a Tool caBIGTM Compatible – Overview |
| Learn more about caBIGTM policies and resources related to data sharing.   | Lesson 7: Focus on caBIGTM Data Sharing and Security Framework |

## In this lesson, we: 

Discussed the goals of caBIGTM and the benefits of getting connected. 
Reviewed key concepts and terms related to the caBIGTM effort.  
Introduced different methods of getting connected with caBIGTM, including adopting caBIGTM tools and adapting existing tools.

The next three lessons will focus on the different tools available from caBIGTM - these focus on connecting with caBIGTM through tools adoption. 

- Discussed the goals of caBIGTM and the benefits of getting connected.
- Reviewed key concepts and terms related to the caBIGTM effort.
- Introduced different methods of getting connected with caBIGTM, including adopting caBIGTM tools and adapting existing tools.
***The next three lessons will focus on the different tools available from caBIGTM - these focus on connecting with caBIGTM through tools adoption. ***

**Lesson Review**

**Lesson 1: Introduction to caBIGTM **

## Lesson 2:  caBIGTM Self-Assessment & Tools Overview

**Lesson 2:  caBIGTM Self-Assessment & ****Tools Overview**

- This lesson begins by pointing to a self-assessment to help identify your readiness to connect with caBIGTM.  Then, we introduce you to the full range of tools available from caBIGTM.  While some organizations will adopt groupings of tools called bundles, others may want to adopt individual tools independent of those bundles.  This lesson will also introduce you to the infrastructure offered by caBIGTM.
- Learning Objectives for this Lesson:
- Point to a caBIGTM Self-assessment
- Point you to a comprehensive list of caBIGTM tools
- Introduce key elements of the caBIGTM Infrastructure
- Introduce the “Bundles” concept

## Starting with a Self-Assessment  

**Getting started with caBIGTM involves three key steps: **** **
**Assess where you are** – What tools and infrastructure does your organization already have?  What’s your level of readiness to engage with caBIGTM?  Want a systematic set of questions to define your starting state? Review caBIGTM Deployment Self-Assessment (PDF).
**Determine where you want to be** – Where are the gaps that caBIGTM may be able to fill?
**Build a plan for getting there – **Decide what you will adopt and adapt, and how you will engage with the Grid.
- Understanding what’s available can help you determine where you are and where you want to go – the rest of this lesson will point you to the tools and infrastructure already available through caBIGTM.

**Lesson 2: caBIGTM Self-Assessment & Tools**

## caBIGTM Website Tools Landing Pages

- Tools pages on caBIGTM website provide a full listing of caBIGTM tools – with information to support their use - Visit **https://cabig.nci.nih.gov/tools/**

**Lesson 2: caBIGTM Self-Assessment & Tools**

## A Look at the caBIGTM Infrastructure

- caGrid (The Grid) and caCORE are two vital resources when connecting with caBIGTM.  We’ll talk more about these later, but visit https://cabig.nci.nih.gov/inventory/Infrastructure/ to preview the caBIGTM infrastructure – the backbone of caBIGTM.

**Lesson 2: caBIGTM Self-Assessment & Tools**

## A Starting List of Candidate Tools

- To help audiences identify related tools more easily, caBIGTM has identified three “tools bundles.” These are a subset of the full list of available caBIGTM tools.
- Two of these bundles include caGrid-enabled software components, which can interoperate or be used in workflows through the caGrid infrastructure.  A third bundle deals with data sharing and compatibility policies.
- Example tools from the three bundles are listed on the next slide:
**Clinical Trials Compatibility Framework **
**Life Sciences Distribution**
**Data Sharing and Security Framework**

**Lesson 2: caBIGTM Self-Assessment & Tools**

## Introducing the Bundles

**Life Sciences Distribution **

**Clinical Trials Compatibility Framework**

**C3PR**
**PSC**
**caAERS**
**caXchange**
**CTODS**
**caGrid**

**Data Sharing and Security Framework**

**CTODS**
**caArray**
**caTissue**
**geWorkbench**
**caGWAS**
**NCIA**
**caGrid**

**caBIGTM Policies**
**Processes and Best Practices**
**Model Documents**
**Trust Fabric**

**More in Lesson 3!**

**More in Lesson 4!**

**More in Lesson 7!**

**Lesson 2: caBIGTM Self-Assessment & Tools**

## In this lesson, we: 

Presented the three central steps to connecting with caBIGTM: Assessing where you are, deciding where you want to go, and planning to get there.
Provided links to existing tools and infrastructure provided by caBIGTM 
Introduced the concept of the caBIGTM bundles to facilitate tools adoption 

The next two lessons will focus more closely on the software bundles related to clinical trials and life science distribution - these focus on connecting with caBIGTM through tools adoption. 

- Presented the three central steps to connecting with caBIGTM: Assessing where you are, deciding where you want to go, and planning to get there.
- Provided links to existing tools and infrastructure provided by caBIGTM
- Introduced the concept of the caBIGTM bundles to facilitate tools adoption
***The next two lessons will focus more closely on the software bundles related to clinical trials and life science distribution - these focus on connecting with caBIGTM through tools adoption. ***

**Lesson Review**

**Lesson 2: caBIGTM Self-Assessment & Tools**

## Lesson 3:  Focus on the Clinical Trials Compatibility Framework 

**Lesson 3:  Focus on the Clinical Trials Compatibility Framework **

- This lesson provides a closer look at the Clinical Trials Compatibility Framework, including the caBIGTM Clinical Trials Suite, which is the software product component of the framework.
- Learning Objectives for this Lesson:
- Describe the Purpose of the Framework and End User Benefits
- Provide an Overview of the Clinical Trials Suite and Supporting Tools
- Review Success Criteria
- Decision Support: Adopt, Adapt or Hybrid

## Welcome to CTMS & Its Goals

- The Clinical Trials Management Systems (CTMS) Workspace oversees the development and integration of tools for the framework.
- Workspace goals include facilitating the following aspects of clinical trials:
- Planning and instantiation of clinical trials (and monitoring of trials once they are instantiated)
- Conduct of clinical trials
- Reporting of clinical trials data to sponsors
- Interoperability
- Increase the ability to share data
- Increase the ability to use the functionality of tools on other systems

**Lesson 3:  Clinical Trials Compatibility Framework**

## Purpose of the Framework

- The caBIGTM Clinical Trials Suite is an integrated, stable, and secure collection of interoperable software tools that support the management of study participant information through the clinical trial lifecycle.
- The current version of the framework enables management of tasks such as:
*Screening and registering* patients for accrual to clinical trials;
*Scheduling and tracking* of patient encounters during the course of a study;
*Integrating laboratory results* with the patient record;
*Tracking* and *managing* adverse events;
*Capturing, storing, analyzing and routing* clinical data in a meaningful manner.

**Lesson 3:  Clinical Trials Compatibility Framework**

## End User Benefits of the Framework

- Adopting the Clinical Trials Compatibility Framework will ultimately facilitate the management of clinical trials.
- The caBIGTM infrastructure supplements the software tools to support communication and security.
- These tools are available at no cost to the end user – they will all be available by early 2008.
- Once installed by an organization, the tools are designed to be used through a standard internet web browser.

**Lesson 3:  Clinical Trials Compatibility Framework**

## caBIGTM Clinical Trials Compatibility Framework Architecture

**Data for Sharing**

**C3PR**

**PSC**

**caXchange**

**CTODS**

**caAERS**

**caAERS: Cancer Adverse Event Reporting System**
**caXchange: Cancer Data Exchange System**
**PSC: Patient Study Calendar**
**C3PR: Cancer Central Clinical Participant Registry**
**CTODS: Clinical Trials Object Data System**
**caGrid: caBIGTM compatible systems architecture**

**caBIGTM Clinical Trials Compatibility Framework Architecture**

**CLINICAL TRIALS **
**COMPATIBILITY FRAMEWORK**

**Data Sharing & Security Framework**

**caGrid**

## Cancer Adverse Event Reporting System (caAERS)

**Cancer Adverse Event Reporting System (caAERS)** – Captures and manages reports describing adverse events that occur during clinical trials.
- Allows the collection, management and querying of adverse event data (both routine and serious)
- Provides configurable rules to facilitate management and reporting of adverse events at protocol, sponsor and institution levels
- Generates customizable reports and submits to external agencies, including generation of NCI and FDA compliant reports.
- Supports regulatory compliance
- Maps to vocabularies and coding systems

**Lesson 3:  Clinical Trials Compatibility Framework**

**Click Here to ****Visit caAERS**
**Tools Page**

*Click above and a new browser tab or window will appear.*

## caXchange

**caXchange - **Facilitates the automatic capture of data from clinical systems and then performs an automatic translation and import to caBIGTM compatible clinical trials databases.
- Enables automatic transfer of clinical data from point-of-care systems in medical centers, such as clinical chemistry lab systems.
- Incorporates caXchange Lab Viewer, allowing viewing of clinical lab data imported from clinical chemistry and other lab systems.
- Labs can be selected for loading into clinical trials databases and/or adverse event reporting systems
- Automatically flags lab values that may indicate toxicities

**Lesson 3:  Clinical Trials Compatibility Framework**

**Click Here to ****Visit caXchange **
**Tools Page**

*Click above and a new browser tab or window will appear.*

## Patient Study Calendar (PSC)

**Patient Study Calendar (PSC)** - Enables clinical trial managers to schedule and manage treatment and care events for participants in a clinical trial.
- Accommodates interventional, epidemiological (and population), and observational studies.
- Represents study workflow in time, process, and phases
- Represents event-driven and date-driven behaviors
- Allows creation, editing, and management of study calendar templates over the lifecycle of a study
- Allows retrospective outcomes review and reporting of calendar activities
- Tracks activities as they occur and provides a framework for reviewing historic study calendar events
- Provides consent / re-consent notification and tracking

**Lesson 3:  Clinical Trials Compatibility Framework**

**Click Here to ****Visit PSC **
**Tools Page**

*Click above and a new browser tab or window will appear.*

## Cancer Central Clinical Participant Registry (C3PR)

**Cancer Central Clinical Participant Registry (C3PR)**** -** Tracks subject registrations to clinical trials.
- Provides repository for participant information across studies, sites, systems, and organizations as well as current enrollment statistics
- Verifies registration criteria (study open, participant eligible, consent received)
- Facilitates Summary 3 & 4 reporting, by providing extracts of data elements needed for these reports
- Manages study personnel who have access to the registry
- Facilitates compliance with Federal regulations including 21 CFR Part 11, HIPAA and Section 508

**Lesson 3:  Clinical Trials Compatibility Framework**

**Click Here to ****Visit C3PR**
**Tools Page**

*Click above and a new browser tab or window will appear.*

## Clinical Trials Object Data System (CTODS)

**Clinical Trials Object Data System (CTODS)** - Enables storing and sharing of clinical trials data in both identifiable and de-identified form.
- Enables data from any Clinical Trials Data Management System (CDMS) or data source to be available to the cancer research community
- Provides the broader cancer research community with de-identified clinical trials data (data that have all patient identification information removed)
- Consistent with the Biomedical Research Integrated Domain Group (BRIDG) model that underpins data interchange standards and technology solutions, which enable harmonization between the biomedical/clinical research and healthcare arenas.
- Note: CTODS was also previously known as CTOM (Clinical Trials Object Model).

**Lesson 3:  Clinical Trials Compatibility Framework**

## Integration and Interoperability Tools

- A vital part of the framework consists of the tools and infrastructure that help you connect local clinical trials data management investments to the caBIGTM network.
- caGrid - caBIGTM-compatible systems architecture
- Clinical Data Management System (CDMS) Integration
- These also provide security features and access controls to ensure protection of human subject information and clinical research data.
- These are covered further on the following two slides.

**Lesson 3:  Clinical Trials Compatibility Framework**

## caGrid

**caGrid** provides the services backbone for data and message exchange across all the tools.
- Connects all the tools in the caBIG Clinical Trials Framework
- Provides common identity and security management across the tools
- Facilitates message transport and routing between systems
- Manages secure access, query and retrieval of data across tools
- Contains an index of registered services
- caGrid is the topic of Lesson 6.

**Lesson 3:  Clinical Trials Compatibility Framework**

**Click Here to ****Visit caGrid Page**

*Click above and a new browser tab or window will appear.*

## CDMS Integration

**Clinical Data Management System (CDMS) Integration** enables the exchange of data between the framework tools and a caBIGTM compatible clinical data management system.
- Data retrieval from CDMS products that use the caBIG Common Data Elements (CDE’s) and standard Case Report Forms (CRF’s)
- Supports conforming CDMS products, such as Cancer Central Clinical Database (C3D)
- Reduces data entry errors and facilitates clinical trials workflows

**Lesson 3:  Clinical Trials Compatibility Framework**

## Installation and Infrastructure Basics

- The caBIGTM Clinical Trials Framework is a series of enterprise applications that must be installed in a sufficiently robust computer server environment.
- Examples of the dependent software that may be required include:
- Apache Ant, Maven, Service Mix, Tomcat
- Java SE Development Kit (JDK)
- MySQL Database, Oracle Database or PostGreSQL Database
- caBIG-compatible Clinical Data Management System (CDMS)

**Lesson 3:  Clinical Trials Compatibility Framework**

## Adoption Success Criteria 

- Successful adoption of the caBIGTM Clinical Trials Framework includes:
- Deploying and integrating one or more components of the caBIGTM framework into the institution’s clinical research enterprise
- Using caBIGTM harmonized Common Data Elements (CDEs) to capture information collected in clinical trials activities.
- Identifying clinical data that can be made available electronically through the caBIGTM data sharing federation

**Lesson 3:  Clinical Trials Compatibility Framework**

## Decision Support: Adopt, Adapt or Hybrid

- Each organization’s circumstances and environment will be unique.
- The caBIGTM Deployment Self-Assessment can help decide whether the path to caBIGTM compatibility lies in:
*Adoption *of the full caBIGTM Clinical Trials Suite
*Adaptation* of existing systems to connect to the Grid.
*Use a Hybrid approach to *facilitate the bridging of existing, non-caBIGTM systems to the caBIGTM infrastructure.
- Organizations can choose which of these paths, or which combination of these paths, best serves their needs.

**Lesson 3:  Clinical Trials Compatibility Framework**

## In this lesson, we: 

Presented the purpose and end benefits of the Clinical Trials Compatibility Framework  
Introduced the tools and infrastructure provided by the framework 
Summarized success criteria related to adopting the framework, and reminded users of the different paths towards that end

- Presented the purpose and end benefits of the Clinical Trials Compatibility Framework
- Introduced the tools and infrastructure provided by the framework
- Summarized success criteria related to adopting the framework, and reminded users of the different paths towards that end

**Lesson Review**

**Lesson 3:  Clinical Trials Compatibility Framework**

**See Also: Getting Connected with caBIGTM Clinical Trials Compatibility Framework (PDF)**

## Lesson 4:  Focus on the Life Sciences Bundle 

**Lesson 4:  Focus on the Life Sciences Bundle **

- This lesson provides a closer look at the Life Sciences software bundle.
**Learning Objectives for this Lesson:**** **
- Describe the Purpose of the Bundle and End User Benefits
- Provide an Overview of Bundle Tools
- Review Success Criteria

## Purpose and End User Benefits

- Modern Cancer Research involves:
- Complex study designs including: capture and refinement of clinical data; and selection of tissue/serum samples for molecular analysis
- High-throughput molecular assays (e.g., RNA microarrays, CHiP on CHiP, Protein gels, spectrometry, SNP chips, etc)
- Sophisticated analyses involving interdisciplinary teams of investigators, and advanced algorithms and software.
- Integration of data and analyses (automated and human)
- The Life Sciences Distribution is a set of tools and infrastructure to provide support for interdisciplinary teams engaged in translational cancer research. It supports:
- Data capture and analysis
- Management of clinical trial and biospecimen resources.
- Sharing of data and interchange of experimental results among geographically distributed teams of interdisciplinary investigators.

**Lesson 4: Life Science Distribution**

## caBIGTM Life Sciences Distribution

**Data for Sharing**

**caArray: Microarray data management system**
**CaTissue: Biorepository management system**
**caGWAS: Cancer Genome Wide Association Studies **
**NCIA: National Cancer Imaging Archive**
**geWorkbench: Microarray gene expression and sequence data management**
**CTODS: Clinical Trials Object Data System**
**caGrid: caBIGTM compatible systems architecture**

**caBIGTM Life Sciences Distribution**

**CTODS**

**caArray**

**caTissue**

**NCIA**

**LIFE SCIENCES **
**DISTRIBUTION**

**caGrid**

**Data Sharing & Security Framework**

**Lesson 4: Life Science Distribution**

## caArray – Microarray Data Management System

**caArray - **Microarray data management system that guides annotation and supports the exchange of microarray gene expression array data
- Provides both web browser-based and programmatic access to microarray data
- Facilitates integration of array data with diverse data types including clinical, imaging, tissue, and other functional genomics data through harmonization with relevant caBIGTM models
- Connects to analytical tools like geWorkbench and GenePattern

**Lesson 4: Life Science Distribution**

**Click Here to ****Visit caArray **
**Tools Page**

*Click above and a new browser tab or window will appear.*

## caTissue Core

**caTissue Core** is a biorepository management that supports collecting, processing, managing, annotating, requesting, and distributing biospecimens and associated information.
- Provides browser-based and programmatic access to biospecimen data
- Provides a means for collecting, processing, storing, and distributing specimens for correlative science cancer research
- Manages tissue, fluid, cell, and molecular biospecimen information
- Allows users to find and request specimens needed for use in molecular correlative studies

**Lesson 4: Life Science Distribution**

**Click Here to ****Visit caTissue Core**
**Tools Page**

*Click above and a new browser tab or window will appear.*

## caGWAS – Managing Large Association Studies

**Cancer Genome-Wide Association Studies** (**caGWAS)** allows researchers to integrate, query, report, and analyze a variety of data types from multiple sources including microarray, genomic, immunohistochemistry, imaging, and clinical data through a single application
- Facilitates rapid sharing of information
- Accelerates the process of analyzing results from various biomedical studies
- Allows researchers and bioinformaticians to access and analyze clinical and experimental data across multiple clinical studies

**Lesson 4: Life Science Distribution**

## NCIA - National Cancer Imaging Archive

**National Cancer Imaging Archive (NCIA)** is a searchable repository of *in vivo *cancer images, such as CT, MRI, and Digital X-rays. NCIA also contains annotation files (PDF, image markup) and annotation data provided by a curator. Cancer images are integrated with clinical and genomic data.
- Enables development of imaging resources that will lead to improved clinical decision support
- Provides an accessible repository for images along with key annotations
- Accelerates diagnostic imaging decision-making and quantitative imaging assessment of drug response
- Serves as a platform for image data management and integration with other research data types

**Lesson 4: Life Science Distribution**

**Click Here to ****Visit NCIA **
**Tools Page**

*Click above and a new browser tab or window will appear.*

## geWorkbench – Expression and Sequence Analysis Tools

**geWorkbench** is a desktop bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization, and annotation of microarray-based gene expression and sequence data.
- Desktop application with a powerful graphical interface
- Enables integrated analysis of genomic data (gene expression, sequence, pathway, structure)
- Brings together analysis and visualization tools for gene expression, sequences, pathways, and other biomedical data
- Provides seamless access to databases, computational services, and biological annotation sources
- Enables sophisticated analysis of genomic data through the integration of visualization tools, external databases, and computational services

**Lesson 4: Life Science Distribution**

**Click Here to ****Visit geWorkbench **
**Tools Page**

*Click above and a new browser tab or window will appear.*

## Clinical Trials Object Data System (CTODS)

**Clinical Trials Object Data System (CTODS)** - Enables storing and sharing of clinical trials data in both identifiable and de-identified form.
- Enables data from any Clinical Trials Data Management System (CDMS) or data source to be available to the cancer research community
- Provides the broader cancer research community with de-identified clinical trials data (data that have all patient identification information removed)
- Consistent with the Biomedical Research Integrated Domain Group (BRIDG) model that underpins data interchange standards and technology solutions, which enable harmonization between the biomedical/clinical research and healthcare arenas.

**Lesson 4: Life Science Distribution**

## caGrid

**caGrid** is a service-oriented architecture and federation that connects caBIGTM-compatible systems together regardless of where they are installed.
- Query across data resources installed in different locations
- Automatically integrate comparable data from different sources
- Create workflow pipelines for data retrieval and analysis using resources across the grid
- caGrid is the topic of Lesson 6.

**Lesson 4: Life Science Distribution**

**Click Here to ****Visit caGrid Page**

*Click above and a new browser tab or window will appear.*

## Bringing Tools Together: Case Study

**Here is a scenario for how these tools might be used together: **
- A Team of Clinical and Basic Science Investigators from multiple Cancer Centers wish to collaborate to discover new candidate genes involved in breast cancer.
- Subjects need to be selected that fit a rigorous profile: CTODS and the NCIA are used to search the databases of the multiple Centers to select the patient pool. caGrid makes it possible for the databases at multiple institutions to be interconnected for a joint search
- Molecular studies at the gene expression and genome structure levels are envisioned for this study. caTissue makes it possible to determine which subjects have suitable tissue and serum samples to permit genome-wide SNP analyses and gene expression profiles before and after treatments.
- caGWAS is used to design and execute the SNP-based study.
- geWorkbench supports a number of analyses related to RNA expression profiles in tissues of affected patients.

**Lesson 4: Life Science Distribution**

## Installation and Infrastructure Basics

- The caBIGTM Life Science Distribution is a collection of diverse applications that require different types and levels of dependent software and infrastructure support.
- Examples of the dependent software that may be required include:
- Apache Ant
- Apache Axis
- Java Development Kit (JDK)
- JBoss Application Server
- MySQL Database
- Hibernate
- Common Security Module: CSM
- Other software: MIRC T29-a and Cedara I-Response Workstation (IRW) (for NCIA)
- Castor (for CTODS)

**Lesson 4: Life Science Distribution**

## Adoption Success Criteria 

- Successful adoption of caBIGTM Life Sciences Distribution includes:
- Deploying and integrating at least one of the caGrid-enabled software applications into the organization’s working activities
- Deploying and maintaining a functional caGrid node at the organization
- Providing access to appropriate real data from the underlying Life Sciences Distribution applications through the caGrid node
- The caBIGTM Deployment Self-Assessment (PDF) can help determine your best path to connecting to caBIGTM and adopting a Life Sciences Distribution tool.
- In addition to adopting one of these tools, you can adapt your own life sciences tool to be caBIGTM compatible.

**Lesson 4: Life Science Distribution**

## In this lesson, we: 

Presented the purpose and end benefits of the Life Sciences Distribution set of tools 
Introduced the tools and infrastructure provided by this tools set 
Summarized success criteria related to adopting the framework, and reminded users of the different paths towards that end

- Presented the purpose and end benefits of the Life Sciences Distribution set of tools
- Introduced the tools and infrastructure provided by this tools set
- Summarized success criteria related to adopting the framework, and reminded users of the different paths towards that end

**Lesson Review**

**Lesson 4: Life Science Distribution**

**See Also: Getting Connected with caBIGTM Life Sciences Distribution (PDF)**

## Lesson 5:  Making a Tool caBIGTM Compatible 

**Lesson 5:  Making a Tool caBIGTM Compatible **

- This lesson provides an overview of the process and criteria for making a tool caBIGTM compatible.  This lesson is for organizations that wish to **adapt** existing tools to be caBIGTM compatible.
**Learning Objectives for this Lesson:**** **
- Introduce Compatibility and the Compatibility Criteria
- Summarize the Compatibility Life Cycle
- List Variables Impacting Compatibility Development Time
- Summarize the Compatibility Review Process

## What is caBIGTM Compatibility? 

- caBIGTM compatibility is about utilizing **standards** to ensure **interoperability** among caBIGTM tools – so that data can be exchanged and understood between systems.

**Lesson 5:  Making a Tool caBIGTM Compatible **

## When Compatibility is Important

- If you are adopting caBIGTM tools, don’t worry about making them caBIGTM compatible.  Compatibility is built in to caBIGTM tools;  look for tools advertised at the “Silver” or “Gold” level.
- You need to make a software tool caBIGTM compatible if:
- If you want to share data (“a data service”) with others via the Grid
- If you want to share data analysis software (“analytical service”) with others via the Grid
- You want to integrate a caBIGTM tool into your organization’s workflow or existing tool base, and exchange data between tools and with the Grid.
- You want to extend or modify an existing open source caBIGTM tool to meet your needs.

**For More Information Access: caBIGTM Compatibility Guidelines **

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Compatibility Guidelines

- Differing degrees of interoperability are assigned based on the tool's adherence to the caBIGTM Compatibility Guidelines.
- There are four different levels of interoperability: Legacy, Bronze, Silver, and Gold. caBIGTM focuses on achieving Silver and Gold compatibility.
- There are four areas of compatibility - an application must meet the guidelines in _all four areas_ to be considered "caBIG Compatible:”

**Semantic Interoperability **
- Information Models
- Vocabularies and Ontologies
- Common Data Elements (CDEs)
**Syntactic Interoperability **
- Programming and Messaging Interfaces (e.g., Application Programming Interfaces)

**Lesson 5:  Making a Tool caBIGTM Compatible **

## How the Compatibility Criteria Work Together

**Information Models** are developed to represent the interfaces of a system. The information model is then annotated with **controlled vocabularies** to establish a foundation of shared meaning for all components of the information model. This annotated information model is then converted into **Common Data Elements** that provide the structure (or format) for the data.
- The information model is really the starting point of all things caBIGTM Compatible.  The information model also serves as the starting point to generate the **API**, which is the mechanism by which the data is exchanged.

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Compatibility Criteria & Resources

- The following four slides introduce the compatibility criteria.  The slides also point to classes in the caCORE curriculum related to the criteria.
- caCORE is composed of a controlled vocabulary repository, and a metadata repository. The caCORE Software Development Kit (SDK) provides tools to generate a caCORE like system, which satisfies silver compatibility.  caCORE classes teach these tools.
**caCORE Courses to Get Started: **** **
- 1000: Intro to caCORE and caDSR
- 1010: Intro to ISO/IEC 11179
- 1020: Using the CDE Browser and UML Model Browser

- The caCORE _Software Development Kit (SDK)_ is an important set of tools used to create a caBIG compatible system.  Using the kit requires intermediate Java development skills.

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Information Models

- Object-oriented model of the system
- Detail associations and relationships between objects
- Objects of system defined by a controlled public vocabulary
- Silver Level Review
- The model accurately **reflects the scientific domain**
**Semantic annotation** is complete and accurate
- UML modeling **best practices** are followed

**caCORE Training Courses:**
- 1070: Curating Metadata from UML Models
- 2010: Using the caCORE Software Development Kit (SDK)

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Vocabularies & Ontologies

- Vocabularies and Ontologies
- Contain agreed-upon concepts, terms, and definitions
- Used to annotate Object Models which results in defined metadata (e.g. CDEs) and Data (e.g., permissible values)
- Agreement upon the basic concepts, terms and definitions that are inherent in all biomedical information is essential for achieving semantic interoperability.

- Silver Level Checklist – Main Points
**Controlled terminologies are used** where appropriate
- All terminologies must be **publicly available**
- Concepts used to annotate classes and attributes must be publicly available and from a designated caBIG Standard vocabulary.

**caCORE Training Courses:**
- 1030: Using Enterprise Vocabulary System (EVS)
- 1040: Creating Well-formed Metadata and Metadata Business Rules

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Common Data Elements

- Metadata description that define and describe data, including data representations like UML models
- Tagged with concepts from accepted vocabularies
- Silver Level Checklist – Main Points
- All attributes are correctly **annotated and loaded** into the caDSR
**Semantic annotation** is complete and accurate
**Value domains are curated** where appropriate
**Data Elements** are reused where appropriate

**caCORE Training Courses:**
- 1070: Curating Metadata from UML Models
- 2010: Using the caCORE Software Development Kit (SDK)

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Application Programming Interfaces

**Application Programming Interfaces**

- Programming and Messaging Interfaces
- Standards-based Application Programming Interfaces (API’s) provide access to data in the form of objects as specified in an UML model
- Standards-based messaging protocols are supported
- Syntax of interfaces are defined by agreed-upon standards
- Silver Level Checklist – Main Points
**API** exists
**API** is well-described and documented
**API** parameters are objects defined by CDEs

**caCORE Training Courses:**
- caCORE SDK Programmers Guide

**Lesson 5:  Making a Tool caBIGTM Compatible **

## The Five Steps to Compatibility

- There are five steps in developing a caBIGTM compatible application – the steps relate to the four compatibility criteria above:
- Creating an Information Model
- Performing Semantic Integration (Vocabularies)
- Transforming the Information Model into Metadata (Common Data Elements)
- Generating Code and Messaging Interfaces (API’s)
- Generating a caGrid Interface

**Lesson 5:  Making a Tool caBIGTM Compatible **

## A Closer Look at the Compatibility Process

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Variables Impacting Development Time

- Past experience has shown that **six** key variables will impact the effort and time required to make a tool caBIGTM compatible:
**Existing familiarity with tools:**  Access to a development team that has knowledge and skills related to UML and CDE models and tools, Enterprise Architect, and NCI tools such as the Semantic Integration Workbench (SIW), caAdapter, and Introduce will help speed development.
**UML modeling skills: **Team understanding and facility with classes, attributes and data types; cardinality; UML structures; understanding of inheritances and associations; and camel case naming conventions will speed development time.
**Projected number of classes and attributes: ** The projected number of classes/attributes for the tool in question will impact development time.
**Technology/Infrastructure:** The following technical environment and infrastructure needs to be in place: Windows, Java WebStart, Internet Explorer 6.0, and the Enterprise Architect software tool.
**Access to Domain Expertise:**  Access to the appropriate domain specialists to support the data modeling effort will facilitate and speed development.
**Time Availability:** Having the team development available to spend concentrated time on the project will help speed efforts.

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Critical Deliverables

- A number of project deliverables help determine whether an application is caBIGTM compatible:
**UML Model** – represents the domain model; and class diagrams for the API
**Annotated XMI file** – used to verify semantic consistency between the UML and CDE definitions; must have clean SIW error log
**UML Loader Checklist** - for registration in caDSR: gives information about the model and constituent packages
**Value Domain Report** – data types and permissible values
**Vocabulary Report **– lists the controlled vocabularies used
**Standard CDE Report** – lists the standard CDEs used and loaded into the caDSR; and reasons for why other standards CDEs could not be used
**CDE Report** – export of all CDEs
**API Documentation** – Documents methods, parameters, messaging interfaces, etc (e.g. JavaDocs)
**Test Scripts** - Establishes existence of API, tests APIs and objects
**Test Log** – From API test scripts, establishes existence

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Compatibility Review Process

- As of October 2007, compatibility reviews for funded caBIGTM projects are conducted through the VCDE and Architecture workspaces.
- This review process may be modified in the future based on demand as more organizations deploy caBIGTM in their environment and adapt their tools.
- If you have questions about the current status of the compatibility process, visit the Compatibility and Certification page of the caBIGTM website.
- The next slide provides a snapshot of the current compatibility review process for reference.

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Compatibility Review Process

**Compatibility Review Process**

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Compatibility Resources

| Reference | Link |
| --- | --- |
| Current Version of Compatibility Guidelines | https://cabig.nci.nih.gov/guidelines_documentation  |
| caCORE Software Development Kit (SDK) | http://ncicb.nci.nih.gov/NCICB/infrastructure/cacoresdk  |
| caDSR Tooling (Semantic Integration Workbench, CDE Browser, UML Model Browser) | http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr   
 |
| caCORE Curriculum
 | http://ncicbtraining.nci.nih.gov/TP2005/tp2000web.dll/NCICBTraining   |

**Lesson 5:  Making a Tool caBIGTM Compatible **

## In this lesson, we: 

Introduced caBIGTM compatibility and the four compatibility criteria
Summarized the Compatibility Development Life Cycle
Listed Variables Impacting Compatibility Development Time
Summarized the Current Compatibility Review Process

- Introduced caBIGTM compatibility and the four compatibility criteria
- Summarized the Compatibility Development Life Cycle
- Listed Variables Impacting Compatibility Development Time
- Summarized the Current Compatibility Review Process

**Lesson Review**

**Lesson 5:  Making a Tool caBIGTM Compatible **

## Lesson 6: Focusing on the Grid

**Lesson 6: Focusing on the Grid**

- This lesson provides a closer look at caGrid.  This topic is critical because “getting on the Grid” is the ultimate target of the compatibility process.
**Learning Objectives for this Lesson:**** **
- Understanding the Grid: What it means to “be on the Grid”
- Implementing caGrid Infrastructure and Tools
- Understanding Grid Security
- Setting up a Grid Node: Overview and Resources
- Surfacing a Grid Data Service

## What is a Grid?

- Grids have evolved from the concept of distributed computing to support science and engineering.
- Key Features and Benefits:
- Sharing of resources (computational, storage, data, etc)
- Secure Access (global authentication, local authorization, policies, trust, etc)
- Open Standards
- Virtualization

- Source: caBIG Annual Meeting 2007: caGrid 1.0 Tutorial Overview

*“**The real and specific problem that underlies the Grid concept is coordinated resource sharing and problem solving in dynamic, multi-institutional virtual organizations.”*
*I. Foster, C. Kesselman, S. Tuecke. International J. Supercomputer Applications, 15(3), 2001. *

**Lesson 6: Focusing on the Grid**

## Grids Help Users Find Services & Data

**Grids Help Users Find Services & Data**

- Metadata (information about the stored data) is deposited in a “Grid index service” that can be queried by grid users (Advertisement and Discovery).

**Tool or Data**

- caBIO
- Grid Service

- Grid Service
- (Metadata & Index Service)

- Source: Modified from caBIG Annual Meeting 2007: caGrid 1.0 Tutorial Overview

- Grid (Client Apps, Users)

**Advertisement ****and Discovery**

**Lesson 6: Focusing on the Grid**

## What is caGrid? 

- caGrid (or the Grid) is an Architecture development project that provides the core infrastructure and tooling needed to connect to the Grid - this is the ultimate target of the compatibility process.
**caGrid and Gold Compliant tools create the *****G***** in caBI*****G******TM***
**G**old => **G**rid => Connecting Silver Systems –** HOWEVER - **
**Grid enabling your tool does NOT make it GOLD compatible.**  Additional criteria at the GOLD level include CDE re-use, CDE standard enforcement, vocabulary standard usage, and model harmonization.
- “Getting something on the Grid” – or “establishing a Grid node” - means meeting requirements for interoperability (through adoption or adaptation), and then connecting that interoperable service or data source to a Grid (internal or external).  Grid services are “advertised” through an index. You can also connect to a Grid to “discover” services or data provided by others.

**Lesson 6: Focusing on the Grid**

## Getting on the Grid: Advertising and Discovering Services

- Source:  caGrid 1.1 Users Guide, Figure 5-2, pg. 42

- Core services – including data standards, shared vocabularies, and indexing – provide the critical elements needed to advertise and discover other Grid resources.

## Getting on the Grid: Key Requirements

**You cannot “get your tool on the Grid” unless you have: (1) adopted or adapted a tool that is caBIGTM compatible; (2) Installed caGrid software. **
- To Grid-enable a system (expose a compatible tool on the Grid) you must:
- Use **object types** and **information models** registered in the caDSR.
- Develop object oriented **APIs** and **data resources**.
- Define a **Grid service interface** that defines the functionality that you are exposing to the Grid. This grid service interface uses the same object types as your existing system, but represents them in a way that is platform and language neutral (e.g., using XML)
- Complete Grid service implementation by **mapping service invocations to API calls or queries** into the existing system
- All of these activities are enabled through caGrid tools and infrastructure – adopting a caBIGTM compatible tool means much of the work has already been done for you – adaptation may take more effort.

- Source: caBIG Annual Meeting 2007: caGrid 1.0 Tutorial Overview

## Getting on the Grid: A Closer Look at the Data 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.  These components are in turn registered in the Cancer Data Standards Repository (caDSR)
- Object definitions draw from controlled terminology and 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)

- Source: caBIG Annual Meeting 2007: caGrid 1.0 Tutorial Overview

## caGrid Infrastructure & Tooling:High Level View

- Ultimately, the Grid consists of a collection of applications and services, connected to each other through a secure infrastructure.

## caGrid Infrastructure & Tooling:Technology Overview

- caGrid 1.1 leverages the following key technologies:

- Source:  _[https://](https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/)__[cabig.nci.nih.gov/workspaces/Architecture/caGrid](https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/)__[/](https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/)_

| Globus Toolkit | Provides the core Grid infrastructure and supports service deployment, service registry, invocation and secure communication | Globus Alliance 
 |
| --- | --- | --- |
| Mobius GME: | Provides grid repository for XML Schemas of strongly typed objects transferred on caGrid | Ohio State University 
 |
| Cancer Data Standards Repository (caDSR) | Provides repository for Common Data Elements and UML models | National Cancer Institute Center for Bioinformatics  |
| Enterprise Vocabulary Services (EVS): | Provides controlled vocabularies | National Cancer Institute Center for Bioinformatics |
| ActiveBPELTM: | Provides an open source workflow engine whose implementation follows the Business Process Execution Language standard | Active Endpoints, Inc. 
 |
| Grouper | Provides ability to manage group information across integrated applications and repositories | Internet2 
 |

## Installing caGrid v1.1

- caGrid 1.1 requires that Java 1.5 JDK be installed on the target machine. Download from _[http://](http://java.sun.com/)__[java.sun.com](http://java.sun.com/)_.
- The caGrid 1.1 installer provides a graphical, wizard-like interface for installing caGrid dependencies, source, services, and applications. Features include:
- Component installers: Install all caGrid services and applications
- Designed for re-use: Can be used to re-install/re-configure previous  installations
- Detailed installation instructions are available online at: _[http://www.cagrid.org/mwiki/index.php?title=CaGrid:Software](http://www.cagrid.org/mwiki/index.php?title=CaGrid:Software)_

- Source: _[http://www.cagrid.org/mwiki/index.php?title=CaGrid:Software](http://www.cagrid.org/mwiki/index.php?title=CaGrid:Software)__ _

**Lesson 6: Focusing on the Grid**

## Grid Installation Wizard

## What About Security?! 

- caGrid uses several packages to provide security services.
**Dorian** allows institutions to locally authenticate their users onto caGrid.
**GridGrouper** group memberships and project access rights to be managed.
**Trust Relationships** specify which institutions trust each other’s authentication.
**GAARDS** was developed on top of the Globus Toolkit and extends the Grid Security Infrastructure (GSI) to 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
- The following figure shows how this all fit together to form a security architecture.

**Lesson 6: Focusing on the Grid**

## caGrid GAARDS Security

**For Explanatory Content Visit: GAARDS Wiki OR ****caGrid 1.1 Users Guide, Figure 6-1, pg. 60**

**Lesson 6: Focusing on the Grid**

## caGrid Security Flows

**For Explanatory Content Visit: Dorian Wiki OR  caGrid 1.1 Users Guide, Figure 6-2, pg. 53**

**Lesson 6: Focusing on the Grid**

## Grid Trust Service - Detail

**For more context, visit:  caGrid 1.1 Users Guide Figure 6-20, pg. 85**

**Lesson 6: Focusing on the Grid**

## Creating a Grid Service

- What kinds of Grid services are there?
- An **Analytical Service** provides operations to perform a particular analysis on data of interest.
- Services providing data resources to the grid are required to be developed as **Data Services**.  In addition to meeting basic service requirements, these must implement a standard query operation and language, and expose standardized data service metadata.
- Why create or access a Grid service?  Here are two use cases related to the bundles introduced earlier:
- geWorkbench can be used to download, view and analyze data stored within caArray.
- Queries could be developed joining clinical annotations from caTissue Core with association data from caGWAS* *(Cancer Genome-Wide Association Studies).* *

**Lesson 6: Focusing on the Grid**

## Creating a Grid Service

- The first step in creating a Grid service is to complete the compatibility process described in earlier lessons.  The caCORE Software Development Kit (SDK) is a useful resource for that process.
- Once you have loaded your data model into caDSR and generated public APIs, the **Introduce Toolkit** supports the next step. Introduce is a graphical development environment, and is one of the Grid services installed when you install caGrid 1.1.
- A Closer Look at the Technical Implications:
- XML Schemas specify how objects are communicated on the grid.  The caCORE SDK can be used to create the XML Schemas.
- If the SDK is not used, then you can either provide an XML schema, or ask Introduce to use the SDK internally to create one.
- Introduce also maps XML to Java beans, which can be preexisting classes (such as those generated by the SDK), or it can generate classes from the XML schemas using Axis. It can also import data types from the caDSR and further customize them as needed.
- (Source: Scott Oster, personal communication; also see caGrid 1.1 User’s Guide, pgs. 15, 18 and 33.)

**Lesson 6: Focusing on the Grid**

## Introduce – Capabilities & Prerequisites

**Why use Introduce?  Here’s a partial set of capabilities: **** **
- Domain Model import from caDSR
- Service creation and modification.
- Import of new data types from GME (global model exchange), file system or other sources.
- Service object code generation if needed.
- Generation of service method stubs – the developer provides the service methods within these.
- Client API generation.
- Configuring security.
- Deploying the service to a container.
- Enabling special data transfer methods such as Bulk Data Transfer or WS-Enumeration.

- Source: _[http://](http://www.cagrid.org/)__[www.cagrid.org](http://www.cagrid.org/)__[ ](http://www.cagrid.org/)_

**Here’s the software recommended for use with Introduce V1.1: **** **
- _[Java 1.5 JDK](http://java.sun.com/j2se/1.5.0/system-configurations.html)_
- _[Ant 1.6.5 or 1.7](http://archive.apache.org/dist/ant/binaries/apache-ant-1.6.5-bin.zip)_
- _[Globus](http://globus.org/)__[ 4.0.x](http://globus.org/)_
- _[Eclipse 3.x](http://www.eclipse.org/downloads/)_ (not required)

**Lesson 6: Focusing on the Grid**

## Introduce Graphical Development Environment

- Includes Graphical User Interface (GUI) for creating and manipulating a grid service.
- Allows you to create a simple service skeleton that a developer can then implement, build, and deploy.
- Automatically generates code for a completely caBIGTM compliant grid service, configured to provide:
- Advertisement
- Standard Metadata
- Security
- Complete Client API

- Source: caBIG Annual Meeting 2007: caGrid 1.0 Tutorial Overview

## Introduce – Setting Up a Service

- Source:  http://www.cagrid.org/mwiki/index.php?title=CaGrid:Tutorials:Services:Beginner:Creating

**Lesson 6: Focusing on the Grid**

## Introduce – Choosing the Data Source

- There are several steps to configuring the new service, only the first is shown here – choosing the type of data source.

- _[Source: http://](source:http://www.cagrid.org/mwiki/index.php?title=CaGrid:Tutorials:Services:Beginner:Configuring)__[www.cagrid.org/mwiki/index.php?title](source:http://www.cagrid.org/mwiki/index.php?title=CaGrid:Tutorials:Services:Beginner:Configuring)__[=](source:http://www.cagrid.org/mwiki/index.php?title=CaGrid:Tutorials:Services:Beginner:Configuring)__[CaGrid:Tutorials:Services:Beginner:Configuring](source:http://www.cagrid.org/mwiki/index.php?title=CaGrid:Tutorials:Services:Beginner:Configuring)_

**Lesson 6: Focusing on the Grid**

## Introduce – Configuring the Data Service

- Source:  caGrid 1.1 Users Guide, Figure 4-1, pg. 32

**Lesson 6: Focusing on the Grid**

## Introduce – Final Notes on Services & APIs

**Invoking Operations on a Service**
- While the grid makes it possible to dynamically invoke services for which a client has no APIs (and this is true for caGrid services), this is generally not the procedure clients or applications follow.  Generally, the API for the service is already available, and is “bound” to the particular service of interest at runtime.
- For example, to query any caGrid Data Service, a common client API can be used, regardless of the type of data it exposes.  Applications built to query data services generally would build against this API. For Analytical Services, however, it is more likely a client API specific to a type of analytical service would be used, and, again, instances of that service would be bound to it at runtime. In both cases, the application developer would just make use of a pre-provided client API.
**Dynamic Invocation for Workflows**
- Constructing a workflow is one instance where a client or application may wish to invoke operations on a service without having previously downloaded a client API.
- The caGrid workflow infrastructure provides the mechanism to describe service invocations using a workflow language (BPEL), and request that the workflow service perform the invocation.
- Further details on the workflow infrastructure can be found in the caGrid 1.1 Programmer’s Guide.

- Source: caGrid 1.1 User’s Guide, pgs. 44-45

**Lesson 6: Focusing on the Grid**

## caGrid Service Layers

- Source: caBIG Annual Meeting 2007: caGrid 1.0 Tutorial Overview

- Here’s how it all folds together.

**Lesson 6: Focusing on the Grid**

## Grid Data Service Layers

## Grid Addendum:  Case Study

- The following slides present a case study related to building a Grid service.  The example relies on caTRIP (Cancer Translational Research Informatics Platform), a platform created by Duke University during the caBIGTM pilot.
- The case study demonstrates the technologies needed for a GUI-based client to perform queries across multiple grid services.  The current version can perform cross-database joins using de-identified medical record numbers.
- Case Study Focus:
- Connecting existing data systems, including basic science data, to enhance patient care
- Initial problem scenario is on *outcome analysis:  *Use data from existing patients to inform the treatment of another patient, leveraging clinical, pathology, tissue, and basic science data
- Scenario:  Patient A enters the clinic.  What treatments were applied with success on other patients with similar characteristics (race, sex, symptoms, pathology results, adverse events, biomarkers)?
- We are grateful for slides from Patrick McConnell at Duke Comprehensive Cancer Center.

**Lesson 6: Focusing on the Grid**

## Overview: Connecting Disparate Data Systems

**Tumor Registry**Diagnosis, Treatment, Recurrence, Follow-up

**CAE**Pathology Biomarkers

**caTissue CORE**Tissue Bank

**caTIES**Pathology Reports

**caIntegrator**SNP Data

- caTRIP

- caTRIP

- caTRIP

- caTRIP

**MRN**

- Source: caTRIP: A translational tool in action – caTRIP_icr_2007_05.ppt

**Lesson 6: Focusing on the Grid**

## caTRIP In-depth Architecture

- MAW3

- Tumor Registry

- Illumina

- caTIES

- CAE

- caTissueCORE

- TR

- CGEMSSNP

-      Duke

- Domain Grid Services

- Distributed Query Engine

- query

- discover

- GUI

- IndexService

- IdPService

- Core Grid Services

- Domain Controller

- authenticate

- caTissue CORE

- caTIES

- CAE

- TR

- caIntegrator

- GridGrouper

- authorize

- Source: caTRIP: A translational tool in action – caTRIP_icr_2007_05.ppt

**Lesson 6: Focusing on the Grid**

## caTRIP In-depth Service Implementation

- domainmodel

- caCORE SDK/Hibernate

- CQL Engine

- database

- Object-relational mapping

- Index Service

- caGrid Data Service

- Distributed Query Engine

- advertise

- advertise

- CQL Query

- Source: caTRIP: A translational tool in action – caTRIP_icr_2007_05.ppt

**Lesson 6: Focusing on the Grid**

## caTRIP caGrid Security

- SAML Assertion

- User Credentials

- Dorian

- Duke Authentication Plugin

- Duke Domain ControllerNT Security

- Grid Data Service

- User Grid Certificate

- CSM

- backenddata

- authentication

- authorization

- GridGrouper

- Trust Fabric

- Source: caTRIP: A translational tool in action – caTRIP_icr_2007_05.ppt

**caTRIP caGrid Security**

**Lesson 6: Focusing on the Grid**

## caTRIP caGrid Security

**caTRIP caGrid Security**

**Authenticate with **
**Local Credential Provider**

**SAML Assertion**

**SAML Assertion**

**Grid **
**Credentials**

**Grid **
**Credentials**

**Should I trust the**
**credential signer?**

**Is **
**Authorized?**

**Is member of?**

- Source: caTRIP: A translational tool in action – caTRIP_icr_2007_05.ppt

**Lesson 6: Focusing on the Grid**

## Technical Details Interfaces and Metadata

- Database

- Database

- Database

**...**

- Grid Service

- Grid Service

- Grid Service

**...**

- Query

- Query

- Query

- Query

- Distributed Query Engine

*Discover Services*

*Discover Metadata*

*Model*

*Register*

*Invoke*

- Source: caTRIP: A translational tool in action – caTRIP_icr_2007_05.ppt

**Lesson 6: Focusing on the Grid**

## caTRIP Extensibility: Creating a New Service

**Prerequisite:** There is some data available in a relational database...
- Domain model
- Create a new domain model (it is easier to reuse one)
- Register it in the caDSR
- Create object/relational mapping (use caCORE SDK or do manually)
- Create Java beans
- Generate Hibernate mappings
- Create grid service
- Use Introduce to generate a data service
- Select the domain model
- Select the caTRIP CQL Processor
- Deploy grid service
- Use Introduce to deploy to your container (Tomcat)
- Add to caTRIP

- Source: caTRIP: A translational tool in action – caTRIP_icr_2007_05.ppt

**Lesson 6: Focusing on the Grid**

## Lesson Review

- In this lesson, we provided a closer look at caGrid by.
- Describing what it means to “be on the Grid”
- Outlining how caGrid is installed
- Introducing the infrastructure and tools that make establishing a grid presence possible
- Reviewing the Grid security architecture
- Discussing how to establish a grid node, so that services can be advertised and discovered.

**Lesson 6: Focusing on the Grid**

## For More Grid Information – Resources & References

**caGrid Websites:**
- _[https://cabig.nci.nih.gov/workspaces/Architecture/caGrid](https://cabig.nci.nih.gov/workspaces/Architecture/caGrid)_ - Primary website, with links to software and documentation
- _[http://cagrid.org](http://cagrid.org/)_ – Primary developer site for caGrid.
- _[https://cagrid-portal.nci.nih.gov/portal](https://cagrid-portal.nci.nih.gov/portal/)__[/](https://cagrid-portal.nci.nih.gov/portal/)_ - Lists available services and participants (under construction)
**caGrid Users Mailing List**
- _[https://list.nih.gov/archives/cagrid_users-l.html](https://list.nih.gov/archives/cagrid_users-l.html)_
- _[cagrid_users-l@list.nih.gov](mailto:cagrid_users-l@list.nih.gov)__ _
**Materials from caBIG Developer’s Boot Camp, April 2007**
- _[https://cabig.nci.nih.gov/training/2007_boot_camp](https://cabig.nci.nih.gov/training/2007_boot_camp)_
**Article about caGrid in Bioinformatics, 2006**
- _[http://bioinformatics.oxfordjournals.org/cgi/content/full/22/15/1910](http://bioinformatics.oxfordjournals.org/cgi/content/full/22/15/1910)_ -

## Lesson 7:  Focus on the caBIGTM Data Sharing and Security Framework

**Lesson 7:  Focus on the caBIGTM Data Sharing and Security Framework**

- This lesson provides a closer look at the Data Sharing and Security Framework, which is designed to facilitate appropriate data sharing between and among organizations by addressing legal, regulatory, policy, ethical, proprietary, contractual, and socio-cultural barriers.
- Learning Objectives for this Lesson:
- Introduce the Data Sharing and Security Framework
- Outline the End User Benefits of Data Sharing
- Learn How to Use the Framework as a Decision Support Tool
- Review the Next Steps toward Adopting the Framework
- This framework was established and is being further developed by the caBIGTM Data Sharing and Intellectual Capital (DSIC) Workspace.

## caBIGTM Data Sharing and Security Framework

**caGrid**

**Data for Sharing**

- When fully developed, the Data Sharing and Security Framework will consist of:
- caBIGTM Policies
- Processes and Best Practices
- Model Documents
- Trust Fabric

**caBIGTM Data Sharing and ****Security Framework**

**COMPATIBLE **
**APPLICATIONS**

**Data Sharing & Security Framework**

## End User Benefits of Data Sharing

**WHY SHARE DATA? **
- The large volumes of research data created by the high throughput genomics and proteomics technologies can best be harvested by teams of individuals - rather than by single PI’s.
- To realize the scientific and public health benefits of translational and personalized medicine, collaboration across and within disciplines is required to leverage broad knowledge and skill bases.
- Data sharing raises the visibility of individual studies and data collections; it opens avenues of data dissemination and validation – leading to more citations in publications and increased prominence.
- Grants from NIH exceeding $500,000 _require_ a plan for data sharing.

**Lesson 7: Focus on the caBIG****TM**** Data Sharing and Security Framework**

## Participating in the DSIC Workspace

- If you are in a Cancer Center participating in the “Getting Connected with caBIGTM” deployment effort, you will need to participate in the activities of the DSIC Workspace in order to facilitate data sharing.
- Your participation will involve assisting with the review and refinement of the tools the Workspace is developing to assist researchers and institutions in their data sharing initiatives.  You will be asked to evaluate using these products in your own institution.
- These DSIC tools include such documents and processes as:
- Using the caBIGTM Data Sharing and Security Framework as a decision support tool
- Model documents such as data sharing plans for use with IRBs, standardized click-through data use agreements between providers and users of data, model informed consent provisions for sharing data via caBIGTM
- Policy papers on topics such as data de-identification, incentives to share data, and timeframes for sharing unpublished data

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

## Understanding the Framework

- You can use the caBIGTM Data Sharing and Security Framework as a decision support tool to facilitate data sharing at your Center by determining which data can be shared and under which type of access and data security controls.  To do so, you will need to assess the sensitivity of the data by using the Framework’s four elements:
**Proprietary Value**
**Data Sensitivity**
**IRB or Institutional Restrictions**
**Sponsor Restrictions**
- The organization assesses the data to be shared along the four elements and assigns a low, medium or high sensitivity rating to the data, which drives the selection of the sharing mechanism.

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

## caBIGTM Data Sharing and Security Framework – Roll-up View

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

## Understanding the Framework

- The organization arrives at an overall level of sensitivity for the data by weighting the outcomes of the four elements according to its own judgment.
- The outcome, that is, a low, medium or high sensitivity rating, determines how the organization wants to control access to that data.
- The organization offering to share data determines the controls on access to that data by determining
- The level of certainty needed regarding the *authentication* of the identity of data users, and
- Whether particular authenticated groups or individuals are *authorized* to access the particular data.
- The levels of security attached to data sensitivities of various levels are informed by guidance from the National Institute of Standards and Technology (NIST).
*The assessment is discussed on the following four slides.*

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

## Proprietary Value

**Relates to the Need for Protection. ** Sample Questions: Are the data subject to a restrictive license?  Do the data relate to an invention report you have, or intend to file, with your institution? Is the study closed?  Are the data or study findings awaiting publication?
- The Framework asks you to select the category of proprietary value that best describes your data:

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

**High – PHI, nonpublic intellectual property**
** ****or other significant restriction**

**Medium ****– Data not yet submitted for publication **

**None/Low – Not subject to ****restrictive license or invention report**

## Data Sensitivity

**Relates to Privacy and Security. **Sample Question: ** **Do federal or state laws or your institution's policies prohibit or restrict disclosure?
- The Framework asks you to select the category of sensitivity that best describes your data:

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

**High Sensitivity - Identifiable Data**

**Medium - Coded/Limited Data Set**

**Low Sensitivity - De-Identified/****Anonymized Data Set**

## IRB or Institutional Restrictions

**Relates to Human Subjects Research Considerations. **Sample Question: ** **Do your institution's or IRB's policies or the applicable informed consent documents explicitly or implicitly restrict or permit disclosure (e.g., “no commercial use”)?
- The Framework asks you to select the level of restriction that best describes your data:

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

**High - Explicit Consent ****Limitations/Restrictions**

**Medium - Policy or Consent **
**Limitations**

**Low - Explicit Permission ****for Registry Participation**

## Sponsor Restrictions

**Relates to Restrictions from Sponsors in Grants and Contracts. **Sample Question: ** **Do the terms and conditions in any sponsored agreements prohibit or restrict disclosure outside the institution or to the Grid?
- The Framework asks you to select the level of sponsor restriction that best describes your data:

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

**High - Classified Research/****Major Restrictions**

**Medium - Delays or Other ****Moderate Restrictions**

**Low - No Restrictions**

## Using the Framework as a Decision Support Tool

- Using the Framework as a decision support tool can help you determine the structures and mechanisms needed to share the data under consideration:
**	**
**	****Note:** Each organization must select the type of agreement that best fits the needs.  The Data Sharing and Security Framework is not a strict policy or guideline.

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

**Standardized Click-Through Terms and Conditions-**
**Some Limitations on Access to the Data**

**Individually Negotiated Bi-Lateral or Multi-Lateral Agreement-**
**More Restricted Access Conditions**

**General Website Terms of Use**
**No Restrictions on Access**

## Next Steps

- If you are in a Cancer Center participating in the “Getting Connected with caBIGTM” deployment effort, complete the following steps to begin implementing the caBIGTM Data Sharing and Security Framework:
- Visit the DSIC Workspace to review workspace activities and identify a qualified Cancer Center representative that can best contribute to the review of future workspace products, such as model documents, policies and best practices.  Much of DSIC’s work occurs in two special interest groups (SIG): the Regulatory SIG and the Proprietary SIG.
- Contact the DSIC WS Lead, Marsha Young (young_marsha@bah.com) with your representative’s name, contact information, and area of interest/expertise.
- Join the DSIC listservs to receive announcements. CABIG_DSIC-L - Data Sharing and Intellectual Capital WorkspaceCABIG_DSIC_PRO_SIG-L - Working Group - Proprietary SIG CABIG_DSIC_REG_SIG-L - Working Group - Regulatory SIG

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

## Lesson Review

- In this lesson, we:
- Presented the purpose of the Data Sharing and Security Framework
- Outlined the benefits of data sharing
- Learned how to use the framework as a data sharing decision support tool
- Summarized the next steps toward adopting the framework

**Lesson 7: Focus on the caBIGTM Data Sharing and Security Framework**

**See Also: Getting Connected with caBIGTM Data Sharing and **
**Security Framework (PDF)**

## Lesson 8:  Conclusion

**Lesson 8:  Conclusion**

- This training program has:
- Described the caBIGTM initiative and its goals.
- Pointed to the location of caBIGTM software tools and described their benefits.
- Explained the roles of interoperability, caGrid, and data sharing in achieving caBIGTM goals.
- Described specific actions that your organization can take to connect with caBIGTM, including adopting caBIGTM tools and adapting your own tools to become caBIGTM compatible.

## Next Steps

- The caBIGTM website is the best centralized resource for more:  _[https://](https://cabig.nci.nih.gov/)__[cabig.nci.nih.gov](https://cabig.nci.nih.gov/)__[/](https://cabig.nci.nih.gov/)_
- To send in a specific question about caBIGTM, write to: _[caBIGconnect@cancer.gov](mailto:caBIGconnect@cancer.gov)_
- The Learning Management System includes both the caCORE training curriculum and self-paced training modules about tools: _[http://ncicbtraining.nci.nih.gov](http://ncicbtraining.nci.nih.gov/)_

**Lesson 8: Conclusion**

## caBIGTM Essentials Training Evaluation

- This training program was developed by the caBIGTM Documentation and Training Workspace, and will be updated as deployment experiences continue.
- The following screens **ask three feedback questions about this training** – your responses will help us better meet community needs.
**Thanks for connecting with caBIGTM! **

**Lesson 8:  Conclusion**

## Training Credits

- This training was developed by the caBIGTM Documentation and Training Workspace.  Special thanks go to:
- Tom Casavant - Holden Comprehensive Cancer Center at the University of Iowa
- Robert Freimuth - Mayo Clinic Comprehensive Cancer Center
- Brooke Hatcher - Booz Allen Hamilton
- Eugene Kraus - Meyer L. Prentis/Karmanos Comprehensive Cancer Center
- Salvatore Mungal - Duke Comprehensive Cancer Center
- Jamie Parker - ScenPro
- Kenneth Smith - Herbert Irving Comprehensive Cancer Center - Columbia University
- Many slides pertaining to caGrid, its architecture, security and its implementation were drawn from publicly available presentations. Original authors included Scott Oster and Shannon Hastings of Ohio State University, and Patrick McConnell of Duke University.  We are grateful for these contributions!
- D&T Workspace Leads:  Leslie Derr (NCI–CBIIT) & Jennifer Tucker (OKA – Otto Kroeger Associates)