# Presentation: 924064

## caBIG® Essentials: Self-Paced Training Program 

**Prepared by the ****caBIG****®**** Documentation and Training ****(D&T) Workspace  ****Last Updated: 24 November 2008**

***Click the right arrow below to advance to the next slide. ***

## Training Topic, Audience & Prerequisites

**Topic Statement:  **This training provides an overview of the caBIG® program.  It introduces caBIG® tools, describes different ways to connect with caBIG®, 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 make decisions about possibly deploying caBIG®.  Specific audiences include leaders charged with planning and guiding caBIG® deployment efforts in their organizations.
**Prerequisites:  **This training does not assume any pre-existing knowledge about caBIG®, though it does assume some familiarity with the cancer research domain.  Those familiar with caBIG® may wish to skip material in Lesson 1 and proceed to later lessons.

## Lesson Plan

**Lesson Plan**

- Lesson 1:  Introduction to caBIG®
- Lesson 2:  Planning for caBIG® Deployment
- Lesson 3:  Adopting caBIG® Tools: Clinical Trials Management
- Lesson 4:  Adopting caBIG® Tools: Life Sciences Distribution
- Lesson 5:  Focus on caBIG® Data Sharing and Security Framework
- Lesson 6:  Adapting a Tool To Be caBIG® Compatible: Overview
- Lesson 7:  Making a Tool caBIG® Compatible: Design Patterns
- Lesson 8:  Connecting to caGrid
- Lesson 9:  Getting Support from caBIG® and Next Steps

## Training Objectives

**Training Objectives**

- Describe the caBIG® initiative and its goals
- Locate caBIG® software tools, so that you can evaluate their benefits and appropriateness against your needs
- Explain the roles of data sharing, interoperability, and the Grid in achieving caBIG® goals
- Evaluate and select specific actions that your organization can take to connect with caBIG®
***This training is designed for people who want to support caBIG******®****** goals by achieving the objectives above.  If you are a member of the general public interested in caBIG******®******, please visit ***_**[http://cabig.cancer.gov](http://cabig.cancer.gov/)**_*** ****** ***
***Note: all links in this training open a new window/tab, so if you follow a link, you can always get back to your launching point in the training. ***

## Lesson 1: Introduction to caBIG®

**Lesson 1: Introduction to caBIG****®**

**This lesson introduces the purpose of caBIG****®**** and provides an overview of what it means to connect with caBIG****®****.  **** **
**Learning Objectives for This Lesson:**** **
- Describe caBIG® and its goals
- Introduce the caBIG® community
- Introduce key caBIG® concepts
- Explain what it means to connect with caBIG®
- Decide where to go next in this training

## caBIG® Vision and Goals

**caBIG****®**** Vision and Goals**

**	**
**	****caBIG****®**** Vision**A virtual network of interconnected data, individuals, and organizations whose goal is to redefine how research is conducted, care is provided, and patients/participants interact with the biomedical research enterprise.
**	****caBIG****®**** Goals**
**Adapt or Build** tools for collecting, analyzing, integrating, and disseminating information associated with cancer research and care
**Connect** the cancer research community through a shareable, interoperable electronic infrastructure
**Deploy and Extend** standard rules and a common language to more easily share information

## How Connecting with caBIG® Benefits You

**Benefits of caBIG****®**** for cancer research organizations: **** **
- Facilitate collaborative research through greater access to research data made available through caBIG® 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 caBIG® 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
**caBIG****®**** addresses a critical problem facing basic and clinical researchers today: an explosion of data that requires new approaches for collection, management, and analysis. **

## caBIG® AccomplishmentsSince 2004....

**Built **a community of 1,000+ individuals and 190+ institutions
**Developed **40+ end-user software applications in discovery, clinical trials management, biospecimen management, and other areas

**Deployed **caGrid, the underlying infrastructure of caBIG®,  to “connect” the community
**Promoting **an ongoing** **cultural shift within the research community

## The caBIG® Community:Sponsor and Workspaces 

**The caBIG****®**** Community:****Sponsor and Workspaces **

**caBIG****®**** is sponsored by the National Cancer Institute (NCI) and is administered by the National Cancer Institute’s Center for Biomedical Informatics and Information Technology. **
**caBIG****®**** priorities are set by the NCI and by groups 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.
*Workspaces conduct regular open teleconferences and face-to-face meetings – visit the caBIG**®** Community Web site to learn more. (*_[https://cabig.nci.nih.gov/](https://cabig.nci.nih.gov/)_*) *

## caBIG® Workspaces: Bringing Together a Range of Stakeholders

- Tissue Banks &
- Pathology Tools (TBPT)https://cabig.nci.nih.gov/workspaces/TBPT

- Integrative Cancer Research (ICR)_[https://cabig.nci.nih.gov/workspaces/ICR](https://cabig.nci.nih.gov/workspaces/ICR)_

- Clinical Trials
- Management Systems (CTMS)_[https://cabig.nci.nih.gov/workspaces/CTMS/](https://cabig.nci.nih.gov/workspaces/CTMS/)_

- Vocabularies & Common Data Elements (VCDE)_[https://cabig.nci.nih.gov/workspaces/VCDE](https://cabig.nci.nih.gov/workspaces/VCDE)_

- In Vivo Imaging_[https://cabig.nci.nih.gov/workspaces/Imaging](https://cabig.nci.nih.gov/workspaces/Imaging)_

- Documentation & Training (D&T)_[https://cabig.nci.nih.gov/working_groups/Training_SLWG](https://cabig.nci.nih.gov/working_groups/Training_SLWG)_

- Data Sharing & Intellectual Capital (DSIC)_[https://cabig.nci.nih.gov/working_groups/DSIC_SLWG](https://cabig.nci.nih.gov/working_groups/DSIC_SLWG)_

- Domain Workspaces

- Cross Cutting & Strategic  Workspaces

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

- Click on any box below to visit the workspace’s home page on the caBIG® community Web site.

## The Enterprise Support Network (ESN) Extends caBIG® Support

- _[Knowledge Centers](https://cabig.nci.nih.gov/esn/knowledge_centers)_ (_[https://cabig.nci.nih.gov/esn/knowledge_centers](https://cabig.nci.nih.gov/esn/knowledge_centers)_)  serve as the nexus for an expanding community employing caBIG® tools, standards, and infrastructure in a specific domain. Knowledge Center staff can provide expert guidance to end users, IT staff and senior decision makers implementing caBIG® tools and infrastructure.
- _[Support Service Providers](https://cabig.nci.nih.gov/esn/service_providers)_(_[https://cabig.nci.nih.gov/esn/service_providers](https://cabig.nci.nih.gov/esn/service_providers)_) are able to provide comprehensive technical support under client-specific agreements.  There are four categories of services offered by caBIG® Support Service Providers:
- Help Desk Support
- Adaptation and Enhancement of caBIG®-Compatible Software
- Deployment Support for caBIG® Software Applications
- Documentation and Training Materials and Services
- _[Learn More About Support Options in Lesson 9](slide123.xml)_

## caBIG® Tools and Infrastructure Are Being Adopted Nationally and Internationally

**caBIG****®**** adoption is unfolding in:**
- 46 NCI-designated Cancer Centers
- 16 NCI Community Cancer Centers
**caBIG****®**** being integrated into federal health architecture to connect Nationwide Health Information Network**
**Global Expansion**
- United Kingdom
- China
- India
- Latin America

**Notes:**

We began planning the caBIG Pilot in 2003, and formally launched it in 2004.  We created a network of participants across the community....and developed our plan of action.  
I’m pleased to announce that we have just published the final Report on the Pilot Phase – it’s hot off the press and you are the first to see it.  There are copies at the registration desk.

Note:  the NCCC’s serve a total population of 12 million people with 27,000 new cancer cases a year.  (info from Maureen Johnson via email)

## Key caBIG® Concepts: Foundations for Getting Connected

**Interoperability**:
- A **caBIG****®****-compatible tool **can interoperate with other compatible tools in the caBIG® program.
- caBIG®-compatible tools may connect to the caBIG® infrastructure backbone – called **caGrid **(or “The Grid”).  A tool that is ready for the Grid is “grid-enabled.”

## Two Pathways To Connect with caBIG® 

**Adopting** a tool involves installing software applications already created by caBIG®, integrating them into your workflow, and connecting to caGrid.
**Adapting** a tool involves building an adapter or otherwise modifying existing software applications to be caBIG®-compatible, and then connecting to caGrid.

## Determining the Best Path

**Determining the Best Path**

_**Adopting**_** may be best **_**if**_**...**
- caBIG® tools fulfill your needs in the domains of clinical trials, molecular research, imaging, and/or biospecimen banking
- End users are open to learning new tools and integrating them in workflows
- Existing technical teams are not positioned to build or reengineer software, but could support a software installation effort
_**Adapting**_** may be best **_**if**_**...**
- Existing technology infrastructure and tools meet user needs and are already integrated into workflows
- Technical team has software development expertise and experience with the NCI’s vocabulary and data model tools/repositories
*	*
*	**You can choose a hybrid approach: ****adopting**** available caBIG® applications and ****adapting**** some of your existing applications.  Which options are best for you?  This training will help determine the best path based on your needs and environment.*

## caBIG® Core Principles

**caBIG****®**** Core Principles**

**Open Access **– caBIG® is open to all, enabling wide-spread access to tools, data, and infrastructure
**Open Development **–  Planning, testing, validation, and deployment of caBIGTM tools and infrastructure are open to the entire research community
**Open Source **– The underlying software code of caBIG® tools is available for use and modification
**Federation **– Resources can be controlled locally, or integrated across multiple sites

## Decide Where To Go Next

| If You Are Interested In... | Visit...  |
| --- | --- |
| Learning more about deploying caBIG® in your organization | Lesson 2 |
| Focusing on caBIG® tools related to clinical trials management  | Lesson 3  |
| Learning more about caBIG® tools related to bioinformatics research, bio-banking, and the Grid  | Lesson 4 |
| Learning more about caBIG® policies and resources related to data sharing  | Lesson 5 |
| Learning about the process for adapting your existing tools to be caBIG®-compatible   | Lesson 6 and 7  |
| Learning about the Grid  | Lesson 8  |
| Learning how to get support in deploying caBIG® | Lesson 9 |

## Lesson 1 Review

**In this lesson, we: **
- Discussed the goals of caBIG® and the benefits of getting connected
- Reviewed key concepts related to the caBIG® effort
- Introduced different methods of getting connected with caBIG®, including adopting caBIG® tools and adapting existing tools
***The next lesson introduces the steps required to connect with caBIG******®****** and deploy its tools and infrastructure. ***

## Lesson 2: Deploying caBIG® 

**Lesson 2: Deploying caBIG****® **

**This lesson describes the steps required to connect with caBIG****®**** and deploy its tools and infrastructure within your organization, and discusses the adopt-adapt decision in more depth. **
**Learning Objectives for This Lesson:**** **
- Introduce success criteria and the roadmap for deploying caBIG®
- Describe the stakeholders needed for deployment
- Summarize the tool “bundles” available for adoption
- Introduce the process of adaptation

## What Does Successful caBIG® Deployment Mean? 

**Take a look at what’s possible through caBIG® deployment:**  See a life cycle demo of caBIG® software tools in use for translational medicine at _[https://webmeeting.nih.gov/p29657145](https://webmeeting.nih.gov/p29657145)_** **

## Process Steps for Deploying caBIG®

**Identify Key Stakeholders **
**Conduct Self-Assessment **
**Determine Goals **
**Create Implementation Plans **
**Implement and Assess**

## 1 - Identify Key Stakeholders

- Those who have deployed caBIG® report that identifying internal stakeholders, learning about their needs, and linking those needs to the benefits of caBIG® is the most time-consuming element of adopt/adapt evaluations and decisions.
- Primary considerations expressed by stakeholders involve:
**Labor Needs **(Technical and End User) – Carefully evaluate use cases, staffing implications, training, and time investment
**Political Awareness **– Be sensitive to ownership and funding dynamics when considering the adapt path
**Alignment with Other Requirements **– Work to understand how caBIG® connects with other research efforts and funded requirements
- Senior level support from Center Directors and Research Program Directors is invaluable in any deployment effort!

## 1 - Identify Key Stakeholders (cont’d)

- Four sets of stakeholders are vital in deploying caBIG® – early involvement will help identify both needs and organizational capability.

| Stakeholder Group  | Role |
| --- | --- |
| Senior Leadership  | Provide vision and direction for the caBIG® deployment.  Help align caBIG® deployment goals with overall organization goals. |
| Domain Leads & Researcher
End User | Primary end users of caBIG® tools and standards.  Identify the use cases and gaps that lead to specific deployment goals, and help make adopt/adapt decisions.   |
| Technologists   | Needed to deploy caBIG® infrastructure and tools. Harmonize local vocabularies, standards, and data models with the caBIG® program. Connect caBIG® support resources with local needs. |
| Policy/Regulatory Stakeholders  | Key influencers include regulatory and legal experts, and policy makers who establish standards for data sharing within the institution.  |

## 2 - Conduct a Self-Assessment 

**Your key stakeholders can assist you in answering important questions to help establish goals. The **_**[caBIG](https://cabig.nci.nih.gov/getting_connected/caBIG_Self_Assessment_Instructions_Worksheet.pdf)**__**[®](https://cabig.nci.nih.gov/getting_connected/caBIG_Self_Assessment_Instructions_Worksheet.pdf)**__**[ Deployment Self-Assessment](https://cabig.nci.nih.gov/getting_connected/caBIG_Self_Assessment_Instructions_Worksheet.pdf)**_** (PDF) is a tool to help gather this information. **
**Starting point thoughts: **
- It is vital to understand what you already have (tools and infrastructure) in identifying what you need.  This self-assessment  will also help “preview” technical and organizational readiness.
- Establishing conceptual support and buy-in at senior levels is critical – _and_ – it is the stakeholders with the domain and technical skills who will ultimately translate that commitment into the tactical action needed.  You need both to be successful.

## 3 – Establish Goals4 – Create Implementation Plans 

**Establishing goals helps you determine where you are going; the Implementation Plan proposes how to get there.**
**Here are links to presentations and templates that will help you create these planning tools.  They were created to support formal Cancer Center Deployment efforts in 2007-2008; however, they are good models for anyone hoping to deploy caBIG****®****. **
**	**** ****Goals Documents**
**Overview Presentation - **_[https://gforge.nci.nih.gov/docman/view.php/196/14475/Goals_Intro.pdf](https://gforge.nci.nih.gov/docman/view.php/196/14475/Goals_Intro.pdf)_
**Goals Template - **_[https://gforge.nci.nih.gov/docman/view.php/196/14476/Goals_Outline.pdf](https://gforge.nci.nih.gov/docman/view.php/196/14476/Goals_Outline.pdf)_
**	**** ****Implementation Planning**
**Overview Presentation – **_[https://gforge.nci.nih.gov/docman/view.php/196/14477/Plan_Intro.pdf](https://gforge.nci.nih.gov/docman/view.php/196/14477/Plan_Intro.pdf)_** **
**Implementation Template - **_[https://gforge.nci.nih.gov/docman/view.php/196/14478/Plan_Template.pdf](https://gforge.nci.nih.gov/docman/view.php/196/14478/Plan_Template.pdf)_** **

## 5 – Implement and Assess

**So far, this lesson has provided an overview of the decisions required and the resources available in order to deploy caBIG®.  **
**Remember, implementing caBIG® consists of three activities: **

## Many Options Are Available: Many Paths for Many Scenarios

**Adopting**
**Adapting**

| Option | Operating Scenario | Recommended Solution |
| --- | --- | --- |
| 2 | You have an existing basic tool that you want to keep.  Examples: Access or mySQL database.   | Become caBIG®-compatible by installing a caBIG® tool with a similar function, and then map your tool to it. You connect to the Grid through the caBIG® tool.   |
| 3 | You have existing tools – more complex than a simple database, with separate modules for reporting and storage (e.g., standard reports are a small extract from a larger system).  | Make the existing tool caBIG®-compatible for standard reports only.  Data generated in required reports would be caBIG®-compatible; the remaining data need not be.  |
| 4 | You have an existing complex informatics tool, but reporting needs vary greatly, and you would like to have the entire system caBIG®-compatible for maximum flexibility.  | Make the full database compatible, by creating an interface that maps the existing tool’s data structures to caBIG® standards.  This is the highest investment solution. |

| Option | Operating Scenario | Recommended Solution |
| --- | --- | --- |
| 1 | You have a paper-based system or a homegrown tool that would not be painful to abandon. | Adopt caBIG® tool or a caBIG®-compatible vendor tool, and migrate existing electronic data to new tool.  |

## Want to Adopt caBIG® Tools?Tools Are Available in “Bundles”

**Want to Adopt caBIG****®**** Tools?***Tools Are Available in “Bundles”*

- To identify popular tools for adoption, caBIG® has identified three “tools bundles.” These are a subset of the full list of available caBIG® tools.   Two of these bundles include caGrid-enabled software components.  A third bundle addresses data sharing and compatibility policies.

## Adopting caBIG® Tools:Supporting Clinical Trials

**Adopting caBIG****®**** Tools:****Supporting Clinical Trials**

**Sample Capabilities and Tools:**
**Adverse event management **(caAERS)
**Clinical data exchange **(caXchange)
**Study participant calendar **(PSC)
**Study participant registry **(C3PR)
**Virtual clinical data warehouse **(CTODS)
**caBIG****®****-compatible systems architecture **(caGrid)
**Integration with caBIG****®****-compatible data management systems**
- Tools pages on the caBIG® Web site provide a full listing of caBIG® tools – with information to support their use. Visit: _[https://cabig.nci.nih.gov/tools/](https://cabig.nci.nih.gov/tools/)_

## Adopting caBIG® Tools:Supporting Life Sciences

**Adopting caBIG****®**** Tools:****Supporting Life Sciences**

**Sample Capabilities and Tools:**
**Microarray data management system **(caArray)
**Microarray gene expression and sequence data management**  (geWorkbench)
**Genome-wide data management system**(caGWAS)
***In vivo***** image repository** (NCIA)
**Biobanking management systems     **(caTissue Core)
**Virtual clinical data warehouse **(CTODS)
**caBIG****®****-compatible systems architecture    **(caGrid)
- Tools pages on the caBIG® Web site provide a full listing of caBIG® tools – with information to support their use. Visit: _[https://cabig.nci.nih.gov/tools/](https://cabig.nci.nih.gov/tools/)_

## More About Adoption

**Many tools in multiple domains are available from caBIG****®**** – tool selection should be based on existing tools and identified needs. **
**Adopting requires the engagement of decision makers and end users to establish how tools might benefit research efforts, and how tools might integrate with existing workflows and processes.   **
**Accessing and installing caBIG****®**** tools will require technical teams that can install and integrate the tool into existing infrastructure.  Most caBIG****®**** tools require open source supporting software. **
**Critical factors influencing the adoption decision include:  **
- Tool functionality;
- Usability; and
- Implementation logistics (such as data migration from existing systems).
-  _[Review Lessons 3 and 4 for more](slide38.xml)_

## Want To Adapt Tools To Become caBIG® Compatible? 

**Some connecting with caBIG****®**** already have cancer research tools that are integrated into existing workflows and infrastructure, exchange data, and meet user needs. **
**In this case, your goal may be to **_**adapt**_** these tools to become caBIG****®****-compatible, so they can interoperate with other tools – both with others in the organization and with other organizations connected to the Grid. **
**Adapting a tool to be caBIG****®****-compatible will allow you to...**** **
- Access data from other Centers, and share data with others – both internally and externally
- Access and share data analysis tools and services with others
- Integrate other caBIG® tools with a compatible tool
- Further extend or modify other caBIG® tools to connect with existing ones

## Adapting Tools for caBIG® Compatibility

**Adapting Tools for caBIG****®**** Compatibility**

**There are four steps to make a tool caBIG****®****-compatible.  These steps are addressed further later in this training.  **
- caBIG® compatibility begins with an _Information Model_.
- The information model is then annotated with _Controlled Vocabularies_ to establish shared meaning across model components.
- This annotated information model is then converted into _Common Data Elements (CDEs)_, providing structure and form for the data.
- The information model is also used to generate the _Application Programming Interface (API)_ used to exchange data.
- 	 *Many tools available for adoption from caBIG® already meet compatibility criteria.  Adapting a tool involves creating a new tool or modifying an existing one to meet these criteria and become caBIG®-compatible.*** **

## Adapting Is a Process with Investment Implications

- Investments are required to adapt a tool to become caBIG®-compatible – the cost depends on tool complexity and the degree to which an information model already has been defined.
**Staffing – **Achieving caBIG® compatibility requires technical and domain teams.  The technical team may include a mix of application developers, data modelers and curators, and database administrators.  The domain team represents the scientific research realm that the tool supports.
**Tools – **The NCI provides a set of tools to support the compatibility development process, as well as a controlled vocabulary repository, and a metadata repository. Previous experience with these tools will facilitate the adaptation process – a training curriculum is available to new users.
- You do not have to reengineer an entire tool to become caBIG®-compatible – there are many alternative approaches.  _[Review Lessons 6 and 7 for more](slide69.xml)_

## Deploying a Grid Node: Connecting with caGrid

**Once a caBIG****®**** tool is adopted or adapted, connect to caGrid: a collection of applications and services connected through a secure infrastructure. **_**[Review Lesson 8 for more](slide96.xml)**_

## For More Information 

**Here are links to three presentations that help people talk about caBIG****®**** with others in their organization.  Each presentation covers a different aspect of the caBIG****®**** deployment process.**** **
- _Talking to Your Center: Senior Leadership_ – Provides background information appropriate for talking with Senior Leaders about the benefits and process of connecting with caBIG®.  Access at _[https://cabig.nci.nih.gov/getting_connected/Talking_To_Your_Center_Leadership.ppt](https://cabig.nci.nih.gov/getting_connected/Talking_To_Your_Center_Leadership.ppt)_.
- _Talking to Your Center: Building a Project Team_ – Provides information about the stakeholders you will need involved to effectively connect with caBIG®.  Access at _[https://cabig.nci.nih.gov/getting_connected/Talking_To_Your_Center_Project_Team.ppt](https://cabig.nci.nih.gov/getting_connected/Talking_To_Your_Center_Project_Team.ppt)_.
- _Talking to Your Center: Understanding the Adopt/Adapt Decision_ – Provides information on the tools available for adoption from caBIG®, and introduces the processes for adapting a tool to be caBIG®-compatible.  Access at _[https://cabig.nci.nih.gov/getting_connected/Talking_To_Your_Center_Adopt_Adapt.ppt](https://cabig.nci.nih.gov/getting_connected/Talking_To_Your_Center_Adopt_Adapt.ppt)_.

## Lesson 2 Review

**In this lesson, we: **
- Introduced success criteria and roadmap for deploying caBIG®
- Described the stakeholders needed for deployment
- Summarized the tool “bundles” available for adoption
- Introduced the process of adaptation
***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 caBIG******®****** through tool adoption. ***

## Lesson 3:  Adopting caBIG® Tools –  Clinical Trials Management

**Lesson 3:  Adopting caBIG****®**** Tools –  Clinical Trials Management**

**This lesson provides a closer look at the Clinical Trials Compatibility Framework, including the caBIG****®**** Clinical Trials Suite, which is the software product component of the framework.  Version 1.1 of the caBIG****®**** Clinical Trials Suite was released in November 2008.   **
**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
- Access more information

## Purpose and End User Benefits of the Framework

- The caBIG® Clinical Trials Compatibility Framework facilitates electronic clinical research data management, and enables the comprehensive sharing and integration of information.  The framework also helps connect software tools to existing data management systems and to the caBIG® infrastructure.
- The caBIG® Clinical Trials Suite (CCTS) is a set of caGrid-enabled tools that securely support clinical trials activities, including registering and tracking patients, managing patient activities and calendars, reporting and tracking adverse events, reviewing laboratory data, transferring data to between applications, capturing and cleaning the clinical data, and analyzing and reporting on the collected data.
- Once installed, CCTS tools are used through a standard internet Web browser. The caBIG® infrastructure supplements the software tools to support communication and security.

## caBIG® Clinical Trials Suite (CCTS) Applications

## Access CCTS Tools: November 2008 Release

**Clinical Participant Registry (C3PR) (version 2.5.2) – **A tool for managing clinical trial patient enrollment data across multiple clinical trials, organizations and sites.  Access at _[https://cabig.nci.nih.gov/tools/c3pr](https://cabig.nci.nih.gov/tools/c3pr)_
**Patient Study Calendar (PSC) (version 2.3.3) **– A tool for creating and editing study calendar templates, generating and viewing prospective calendars of patient activities, tracking activities as they occur, and managing patient calendars as they change during a study.  Access at _[https://cabig.nci.nih.gov/tools/PatientStudyCalendar](https://cabig.nci.nih.gov/tools/PatientStudyCalendar)__ _
**Adverse Event Reporting System (caAERS) (version 1.5.1) **– A tool for collecting, managing, processing and reporting routine and serious adverse events that occur during clinical trials.  Access at _[https://cabig.nci.nih.gov/tools/caAERS](https://cabig.nci.nih.gov/tools/caAERS)_

**Clinical Data Exchange (caXchange) (version 1.5.0) **– A configurable hub for exchanging clinical trial information between applications and systems.  Access at _[https://cabig.nci.nih.gov/tools/LabIntegrationHub](https://cabig.nci.nih.gov/tools/LabIntegrationHub)_
**CTODS Lab Viewer (version 1.5.0) **– The Lab Viewer interface allows users to view and query laboratory data in the Clinical Trials Object Data System (CTODS) and select subsets of tests to be sent to a clinical trials database.  This release also includes the Cancer Center Hub Client (CCHS) for batch loading labs and converting them from HL7 v2 to HL7 v3.  Access at _[https://cabig.nci.nih.gov/inventory/infrastructure/CTODS](https://cabig.nci.nih.gov/inventory/infrastructure/CTODS)_
**C3D Connector (version 1.2.0**) – A BRIDG-based adapter that allows applications in the caBIG® Clinical Trials Suite to share information with the C3D Clinical Data Management System.  It can also be configured to operate with other Clinical Data Management Systems.

## A CCTS Use Case...How the Pieces Connect 

- When a patient visits a clinic and signs the consent form, the next step is to register the patient in the Cancer Central Clinical Participant Registry (C3PR), which links the patient to a study and an organization.
- When we assign the patient to a Treatment Epoch in C3PR, the patient registration is broadcasted to the other Cancer Clinical Trial Suite applications through caXchange.
- The Patient Study Calendar (PSC) automatically generates a schedule for the patient, based upon the protocol’s study template and the assigned treatment arm.
- The patient registration information is also sent to both the Cancer Central Clinical Data Management System (C3D) – our Clinical Data Management System – and the Cancer Adverse Event Reporting System (caAERS).
- The patient identifier that was entered in C3PR also links the patient’s labs in the Clinical Trials Object Database System (CTODS).  The labs can then be viewed by the Site Coordinator using Lab Viewer.  In the Lab Viewer Tool, the Coordinator can select the appropriate labs that should be sent to the CDMS and transfer them to the CDMS.
- Both routine and expedited adverse events can be entered in the Cancer Adverse Event Reporting System (caAERS). caAERS can be used to generate the appropriate expedited reports, and can send an alert to the Patient Study Calendar, so the coordinator can decide whether to update the patient’s calendar if necessary.

## Integration and Interoperability Tools

**Integration and ****Interoperability Tools**

- A vital part of the framework consists of the tools and infrastructure that connect local clinical trials data management investments to caBIG®. These include **caGrid**** and ****Clinical Data Management System (CDMS) Integration****.**
**caGrid** provides the services backbone for data and message exchange across caBIG® tools.
- Provides common identity and security management across the tools
- Facilitates message transport and routing between systems
- Manages secure access, query and retrieval of data
- Contains an index of registered services
**Clinical Data Management System (CDMS) Integration**** **enables data exchange between framework tools and a caBIG® compatible clinical data management system.
- Data retrieval from CDMS products that use caBIG ® Common Data Elements and standard Case Report Forms
- Supports conforming CDMS products, such as Cancer Central Clinical Database
- Reduces data entry errors and facilitates clinical trials workflows

## Installation and Successful Adoption

**The caBIG****®**** Clinical Trials Framework is a series of enterprise applications that must be installed in a sufficiently robust computer server environment.  Examples of dependent software 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)
**Successful adoption of the caBIG****®**** Clinical Trials Framework includes:**
- Deploying and integrating one or more components of the caBIG® framework into the institution’s clinical research enterprise
- Using caBIG® harmonized Common Data Elements (CDEs) to capture information collected in clinical trials activities
- Identifying clinical data that can be made available electronically through the caBIG® data sharing federation

## Lesson 3 Review: Learning More About CCTS Tools 

- Where does the path to caBIG® compatibility lie for your organization? You can adopt the full Clinical Trials Suite, adapt existing systems to connect to the Grid, or use a hybrid approach to facilitate the bridging of existing, non-caBIG® systems to the caBIG® infrastructure.

| Resource | Link |
| --- | --- |
| Access the full list of CCTS tools – With links to tool pages and tool demos (including an integrated Suite demo)  | https://cabig.nci.nih.gov/tools/toolsuite_view#CCTS  |
| caBIG® Clinical Trials Management Systems (CTMS) Knowledge Center | https://cabig-kc.nci.nih.gov/CTMS/KC/index.php/Main_Page  (paste link in browser) |
| Getting Connected with caBIG® Clinical Trials Compatibility Framework Fact Sheet (PDF) | https://cabig.nci.nih.gov/getting_connected/1_ClinicalTrial_bundle_LOWres.pdf  |

## Lesson 4:  Adopting caBIG® Tools – Life Sciences Distribution

**Lesson 4:  Adopting caBIG****®**** Tools – Life Sciences Distribution**

**This lesson provides a closer look at the Life Sciences Distribution (LSD) software that can be adopted from caBIG****®****. LSD Version 1.1 was released in October 2008.  **** **
**The LSD is a comprehensive set of tools that support biomedical research, from tracking and managing biospecimens, to analyzing and integrating microarray data.**
**Learning Objectives for this Lesson:**** **
- Describe the purpose of the bundle and end user benefits
- Provide an overview of bundle tools
- Find more information

## Purpose and End User Benefits

**Modern Cancer Research involves:**
- Complex study designs including the 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 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

## Life Science Distribution Tools

**geWorkbench (version 1.6): **A platform for genomic data analysis; includes collection of tools for the management, analysis, visualization, and annotation of microarray-based gene expression and sequence data.  Access at _[https://cabig.nci.nih.gov/tools/geWorkbench](https://cabig.nci.nih.gov/tools/geWorkbench)_
**Life Science Distribution Browser (LSDB) (version 1.0): **A Web front-end to perform keyword searches on local or remote grid-enabled LSD services. This first release supports searching across NCIA and caArray.  Access at _[https://cabig.nci.nih.gov/tools/LSDB/](https://cabig.nci.nih.gov/tools/LSDB/)_
**caArray (version 2.1.1): **The newest version of NCI’s array data management software, that guides annotation and supports the exchange of microarray gene expression array data.  Access at _[https://cabig.nci.nih.gov/tools/caArray](https://cabig.nci.nih.gov/tools/caArray)_
**National Cancer Imaging Archive (NCIA) (version 4.0):** The NCI’s repository for DICOM-based images and the **MIRC** data submission software.  Access NCIA at _[https://cabig.nci.nih.gov/tools/NCIA](https://cabig.nci.nih.gov/tools/NCIA)_ and MIRC at _[http://mirc.rsna.org/](http://mirc.rsna.org/)_

**Clinical Trials Object Database Systems (CTODS) (version 1.0): **Enables storing and sharing of clinical trials data in both identifiable and de-identified form.** **This release includes data loading scripts.  Access at _[https://cabig.nci.nih.gov/inventory/infrastructure/CTODS](https://cabig.nci.nih.gov/inventory/infrastructure/CTODS)_
**caGWAS (version 1.0.1): **A version of the NCI’s caIntegrator platform that supports Genome Wide Association Studies such as the Cancer Genetic Models of Susceptibility (CGEMS) data.   Access at _[https://cabig.nci.nih.gov/tools/caGWAS](https://cabig.nci.nih.gov/tools/caGWAS)_
**caTissue Core (version 1.2.2): **A biorepository management system that supports collecting, processing, managing, annotating, requesting, and distributing biospecimens and associated information.  This version is caGrid-enabled.  Access at _[https://cabig.nci.nih.gov/tools/catissuecore](https://cabig.nci.nih.gov/tools/catissuecore)_

## Learning More About Life Science Distribution Tools

- The tools in the LSD are intended for use by research scientists, and each provides an end user-oriented graphical user interface.
- Each of the data management tools has a Java-based Application Programming Interface (API) and a caGrid-compatible Grid Service for programmatic access to data.
- All of the applications are built on a common set of Open Source technologies for ease of installation and maintenance.
- Components of this bundle can be downloaded from:  _[http://ncicb.nci.nih.gov/download/downloadlsd.jsp](http://ncicb.nci.nih.gov/download/downloadlsd.jsp)_.

## 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 wishes to collaborate to discover new candidate genes involved in breast cancer.
- Subjects need to be selected who 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 level 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.
- caGWAS is used to design and execute the SNP-based study.
- geWorkbench supports a number of analyses related to gene expression profiles in tissues of affected patients.

## Installation and Infrastructure Basics

**The caBIG****®**** 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 Review: Learning More About LSD Tools

- Where does the path to caBIG® compatibility lie for you? You can adopt life tools, adapt existing systems to connect to the Grid, or use a hybrid approach.

- Where does the path to caBIG® compatibility lie for you? You can adopt life tools, adapt existing systems to connect to the Grid, or use a hybrid approach.

| Resource | Link |
| --- | --- |
| Access the full list of Life Science Distribution tools – With links to tools pages and demos | https://cabig.nci.nih.gov/tools/toolsuite_view#LSD   |
| caBIG® Molecular Analysis Knowledge Center | https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page  (paste link in browser) |
| caBIG® Tissue/Biospecimen Banking and Technology Tools Knowledge Center  | https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/Main_Page  (paste link in browser) |
| Getting Connected with caBIG® Life Science Distribution Fact Sheet (PDF) | https://cabig.nci.nih.gov/getting_connected/2_LifeSciences_bundle_LOWres.pdf  |

## Lesson 5: Focus on the caBIG® Data Sharing and Security Framework

**This lesson provides a closer look at the Data Sharing and Security Framework (DSSF), which is designed to facilitate appropriate data sharing among organizations by addressing legal, regulatory, policy, ethical, proprietary, contractual, and socio-cultural barriers.**
**Learning Objectives for this Lesson:**** **
- Outline the benefits of data sharing
- Present the purpose of the Data Sharing and Security Framework
- Introduce the tools being developed to address the legal and cultural barriers to data sharing
- Discuss the technical issues in ensuring secure data exchanges
**This framework was established and is being further developed by the caBIG****®**** Data Sharing and Intellectual Capital (DSIC) Workspace and the DSIC Knowledge Center. **

## Benefits of Data Sharing

**One of the primary goals of caBIG****®**** is to enable and promote data sharing. This is important because:**** **
- The large volumes of research data created by high throughput genomics and proteomics can best be harvested by teams.
- Translational and personalized medicine promise great benefits.  Realizing these benefits requires that collaboration occur both within disciplines and between disciplines, harnessing the broadest possible knowledge and skill bases.
- Data sharing raises the visibility of individual studies and data collections, and opens avenues for data dissemination and validation.
- Grants from NIH exceeding $500,000 require a plan for data sharing.

## Barriers to Sharing Data

**Historically, there have been a number of legal, cultural, and technical barriers to data sharing:**** **
- Varying obligations under federal and state privacy and security laws and standards
- Varying local requirements and oversight of human subjects research by ethical review boards
- Traditional academic reward structures driven by individual success, rather than team-based work
- Researcher, institutional, and sponsor concerns about the protection of intellectual property
- Patient safety concerns related to premature access to unvalidated information
- Public perceptions regarding privacy, security, and confidentiality of electronic health data

## Data Sharing and Security Framework (DSSF)

**Designed to facilitate appropriate data sharing among organizations by addressing legal, regulatory, policy, ethical, proprietary, contractual, and socio-cultural barriers.**
**Offers resources to address the potential and perceived restrictions on data sharing:**** **
- Tools to evaluate the sensitivity of data
- Tools to expedite data sharing arrangements between organizations
- Guidance documents and white papers to inform institutions on data sharing practices
**Offers technology infrastructure to facilitate appropriate access to data:**
- Policies to assure that organizations adhere to security standards
- Tools to implement federated authentication and authorization

## caBIG® Data Sharing and Security Framework (DSSF)

**The Data Sharing and Security Framework includes:**
**Resources to address the legal and cultural barriers to data sharing: **** **
- Tools to evaluate the sensitivity of data
- Tools to expedite the execution of data sharing agreements between organizations (guidelines for data sharing plans)
- Tools to capture patient consent to share data (model informed consent forms)
- Other model documents and white papers to inform institutions on data sharing issues
**Technology infrastructure to ensure secure data exchanges:**** **
- Tools to implement federated authentication and authorization
- Policies to assure that organizations adhere to security standards (Grid Host Agreement)

## Resources to address the legal and cultural barriersGoal of the DSSF: Selecting Access Controls

**The appropriate mechanism for sharing data depends in part on the nature of the data to be shared:  **** **
- Does it contain personal health information?
- Does it contain proprietary information?
- Does it relate to a closed study?
**Depending on the answers to these and other questions, it may be appropriate to share data:**** **
- Publicly, without access controls;
- Via a standard data sharing agreement between organizations; or
- Via a customized data sharing agreement between organizations
**caBIG****®**** developed the DSSF to help organizations determine the access controls needed for any given set of data.**

## Resources to address the legal and cultural barriersUnderstanding the DSSF Levels

**Resources to address the legal and cultural barriers****Understanding the DSSF Levels**

**Each data element is evaluated **
**in terms of four domains:**
- Economic/Proprietary
- Privacy Considerations
- IRB/Ethical Restrictions
- Sponsor Restrictions

- ...and three levels of sensitivity:Low, Medium and High

## Resources to address the legal and cultural barriersHow Data Sensitivity Relates to Access Controls

**Based on this evaluation, the required access controls can be determined:**

## Resources to address the legal and cultural barriersRecap of How the Data Sensitivity Evaluation Framework is Used

**For the data being considered, assess sensitivity for each principal element:**** **
- Economic/Proprietary Value (to Researcher/Institution)
- Privacy Considerations
- IRB/Ethical Restrictions
- Sponsor Restrictions or Requirements
**Assign a ****low (green)****,**** ****medium (yellow)**** or ****high (orange)**** sensitivity rating to the data**** **
**Use sensitivity analysis to determine (1) security/data access controls; and (2) the possible type of data sharing agreements **** **
***The institution providing the data makes this determination!***

## Resources to address the legal and cultural barriersGuidelines for Data Sharing Plans

**On the basis of applying the DSSF, an organization may determine that a data sharing plan is required.  caBIG****®**** supplies guidelines for developing such plans.**** **
**The guidelines provide a framework for organizing information about the data to be shared, and the designated mechanism for sharing:**** **
- Background about the project that will use caBIG® infrastructure
- Issues that drive legal/regulatory determinations such as summary of data elements, intended recipients, mechanisms for data sharing (access controls, agreements), timing, objectives of the project, and who may have interest in the data
- Information about institutional units that must approve data sharing plans
- Open-ended questions regarding additional anticipated challenges

## Resources to address the legal and cultural barriersModel Informed Consent/Authorization

**In some instances, patient consent must also be obtained for data sharing. caBIG****®**** supplies model language for such consents.**
**Model language about caBIG****®**** to use in pre-existing authorization/consents**
- Provide basic language to facilitate data sharing within their own documents; facilitate adoption of caBIG® language in other models
**Standardized choices for research participants related to specimen use and/or data sharing **
- Standardize choices in authorization/consent forms; facilitate adherence to patient/participant choices
**Model informed consent and HIPAA authorization document – “the whole package” (disclosure and options)**
- Assist institutions and smaller provider-based participants in drafting informed consent/authorization forms compliant with Common Rule, FDA and HIPAA requirements

## Technology infrastructure to ensure secure data exchanges Security Basics:  Authentication and Authorization

**In addition to data sharing plans and consents, a technology infrastructure is needed to ensure secure data exchange.**
**The fundamental security issues are:**** **
- Authentication / identity management: How can an organization sharing data be sure that a user is who he claims he is?
- Authorization / privilege management: Once a user’s identity is assured, how can an organization sharing data be sure that he will be allowed access to only the agreed-upon data?

## Technology infrastructure to ensure secure data exchanges Authentication

**Authentication is the process of verifying that a user is who he claims to be. **Typically, a user presents credentials to an entity that is responsible for authenticating.  If the credentials are accepted, the entity issues a “certificate.” Credentials can include: Something you know (a password); Something you are (a fingerprint); or Something you have (a hardware key).
- Different data sharing scenarios require different levels of assurance about authentication.  The level of assurance about authentication can be increased by: (1) Using factors that are not easily shared (a fingerprint, a one-time password, a hardware key); and (2) Requiring multiple credentials.
**caBIG® will use the levels of assurance specified in the Federal E-Authentication Initiative **_**[http://www.cio.gov/eauthentication/](http://www.cio.gov/eauthentication/)**__** **_
- Level 1 –  e.g., no identity vetting is performed
- Level 2 –  e.g., one credential is required
- Level 3 –  e.g., multiple credentials are required
- Level 4 –  e.g., multiple credentials are required and one must be a                   hardware token

## Technology infrastructure to ensure secure data exchanges Authorization

**Authorization is the process of determining if an *****authenticated***** person qualifies to conduct certain activities in cyberspace. **
**The process of authorizing a user is:**
- The user wishing to access data sends his authentication certificate to the organization that owns the data.
- The organization that will be sharing data sends this authentication certificate on to a “source of authority” (SOA), which will determine whether that user qualifies for access to the data.
- The SOA uses the authentication certificate to check whether it “knows” this user.
- If it does, the SOA then checks whether the identified person qualifies for access to the data.
- The SOA sends its determination to the organization that will be sharing the data.
- Based on this determination, the organization either allows or forbids access to the data.
**The institution that is the steward of the data authorizes who can access the data. The SOA is simply the mechanism that sends the authentication credentials back and forth.  **

## Technology infrastructure to ensure secure data exchanges Federated Security, the Trust Fabric

**Past data sharing has been implemented via custom bilateral or multilateral communication, but this approach is not scalable.**
**caGrid is built to support federated authentication and authorization whereby organizations can accept authentication and authorization performed at other organizations.**
- Technical components of the caGrid support for federated authentication and authorization are described in the lesson on caGrid.
**Organizations hosting a grid node must sign the Grid Host Agreement, a set of policies to assure that organizations adhere to security standards.**
**The network of mutual trust relationships among organizations regarding authentication and authorization is sometimes called the “Grid Trust Fabric.”**

## Lesson 5 Review: Learning More About the DSSF

- Learn more about existing tools in the DSSF and the work that is being done on future tools.

| Resource | Link |
| --- | --- |
| caBIG® Data Sharing and Intellectual Capital Workspace | https://cabig.nci.nih.gov/working_groups/DSIC_SLWG/  |
| caBIG® Data Sharing and Intellectual Capital Knowledge Center | https://cabig-kc.nci.nih.gov/DSIC/KC/index.php/DSIC_Tools (paste link in browser) |
| caBIG® Data Sharing and Security Framework (DSSF) Webcast Materials | https://cabig.nci.nih.gov/working_groups/DSIC_SLWG/DSSF_Webcast  |
| Getting Connected with caBIG® Data Sharing Fact Sheet (PDF) | https://cabig.nci.nih.gov/getting_connected/3_DataSharing_bundle_LOWres.pdf  |

## Lesson 6: Adapting a Tool To Be caBIG®-Compatible – Overview

**Lesson 6: Adapting a Tool To Be caBIG****®****-Compatible – Overview**

**This lesson provides an overview of the process and criteria for adapting an existing tool to make it caBIG****®****-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 caBIG® Compatibility? 

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

## When Compatibility Is Important

**When Compatibility Is Important**

**If you are adopting caBIG****®**** tools, do not worry about making them caBIG****®****-compatible.  Compatibility is built in to most caBIG****®**** tools; look for tools advertised at the “Silver” or “Gold” level. **
**You need to make a tool caBIG****®****-compatible and grid-enabled 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 caBIG® tool into your organization’s workflow or existing tool base, and exchange data between tools and the Grid
- You want to extend or modify an existing open source caBIG® tool to meet your needs
- For More Information Access: caBIG® Compatibility Guidelines at _[https://cabig.nci.nih.gov/guidelines_documentation](https://cabig.nci.nih.gov/guidelines_documentation)_

## Compatibility Guidelines

**Differing degrees of interoperability are assigned based on the tool's adherence to the caBIG****®**** Compatibility Guidelines. **
- There are four different levels of interoperability: Legacy, Bronze, Silver, and Gold. caBIG® 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)

## 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 caBIG®-compatible.  The information model also serves as the starting point to generate the **API**, which is the mechanism by which the data is exchanged.

## Compatibility Criteria & Resources

**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.  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
- 	To learn more about these tools and training opportunities visit the caCORE Wiki at _[https://wiki.nci.nih.gov/display/caCORE/CORE+Wiki](https://wiki.nci.nih.gov/display/caCORE/CORE+Wiki)_

## Information Models

**Information Models**

**Information Models**
- Object-oriented model of the system
- Detail associations and relationships between objects
- Objects of system defined by a controlled public vocabulary
**caCORE Training Courses:**
- 	1070: Curating Metadata from UML Models
- 	2010: Using the caCORE Software
- 	Development Kit (SDK)

## Vocabularies & Ontologies

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

## Common Data Elements

**Common Data Elements**

**Common Data Elements**
- Metadata descriptions that define and describe data, including data representations like UML models
- Tagged with concepts from accepted vocabularies
**	****caCORE Training Courses:**
- 1070: Curating Metadata from UML Models
- 2010: Using the caCORE Software
- 	Development Kit (SDK)

## Application Programming Interfaces

**Application Programming Interfaces**

**Programming and Messaging Interfaces**
- Standards-based Application Programming Interfaces (APIs) 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
**	****caCORE Training Courses:**
- 	caCORE SDK Programmers Guide

## The Five Steps to Compatibility

**There are five steps in developing a caBIG****®****-compatible application – the steps relate to the four compatibility criteria above:**** **
- Creating an Information Model in a modeling tool
- Performing Semantic Integration (Vocabularies) using the Semantic Integration Workbench(SIW)
- Transforming the Information Model into Metadata (Common Data Elements) using the UML Loader
- Generating Code and Messaging Interfaces (APIs) using caCORE SDK Code Generator
- Generating a caGrid Interface using “Introduce”

## A Closer Look at the Compatibility Process

## Variables Impacting Development Time

**Past experience has shown that six key variables impact the effort and time required to make a tool caBIG****®****-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 need 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.

## Critical Deliverables

**A number of project deliverables, reviewed by caBIG****®**** experts, determine whether an application is caBIG****®****-compatible: **
**UML Model** – Represents 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 why other standard 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 6 Review: Learning More About Compatibility

**Here are resources to get you started on the path to compatibility – the next lesson explores different ways of looking at compatibility at the design level. **

| Resource |
| --- |
| Current Version of Compatibility Guidelines -  https://cabig.nci.nih.gov/guidelines_documentation  |
| The caCORE UML browser (https://cabig.nci.nih.gov/tools/umlmodelbrowser) is a great resource when you are adapting a legacy tool and want to: 
Identify the CDEs that make up the database schema of an existing caBIG®  tool
Determine degree of overlap between the data fields/elements of a caBIG® tool with a legacy tool  
Conduct a mapping exercise to connect a legacy database to a caBIG® database  |
| Vocabulary Knowledge Center -  https://cabig-kc.nci.nih.gov/Vocab/KC  |
| caCORE and Infrastructure Wiki  - https://wiki.nci.nih.gov/display/caCORE/CORE+Wiki  |
| caCORE Curriculum - http://ncicbtraining.nci.nih.gov/TP2005/tp2000web.dll/NCICBTraining   |

## Lesson 7:  Making A Tool caBIG® Compatible – Design Patterns

**Lesson 7:  Making A Tool caBIG****®**** Compatible – Design Patterns**

**Adaptation is a strategy for connecting to caGrid that enables collaboration on a range of clinical data.  Building on the last lesson, this section outlines possible adaptation strategies.**
**Learning Objectives for this Lesson: **
- Review possible strategies for adaptation: Design Patterns
- A closer look at variables and issues
- Get more information

## Review: Adaptation is Making a Tool caBIG®-Compatible

**caBIG****®**** compatibility begins with an Information (or Data) Model, which represents the interfaces and relationships of a system. **
**The information model is then annotated with Controlled Vocabularies to establish shared meaning across model components (called “semantic integration”). **
**This annotated information model is then converted into Common Data Elements (CDEs) that provide the structure (or format) for the data.  **
**The information model is also used to generate the Application Programming Interface (API): the mechanism by which data are exchanged. **

## Design Pattern Overview

**Design Pattern Overview**

**The following slides outline SIX different approaches for adapting a tool to be caBIG****®****-compatible.  These are conceptual models**** – ****foundational strategies**** – ****for shaping an adaptation roadmap.  This is neither an exhaustive nor mandated list**** – ****it simply provides examples that we believe can facilitate adaptation based on experience to date.**
**	****Understanding Design Patterns **
- 	The six approaches offered here are based on the concept of **design patterns**, which Wikipedia defines as “a general reusable solution to a commonly occurring problem in software design.”
- 	Design patterns are essentially templates: standardized conceptual solutions that can be applied to many different situations. Based on caBIG® experiences, there are six standard ways to approach the software design problems presented by the adapt path identified. These are presented in the following slides.
- http://en.wikipedia.org/wiki/Design_pattern_%28computer_science%29

## 1: Wrapper

**Use Scenario:  There is a desire to continue using an existing legacy tool, without adopting one from caBIG****®****.  In this case, a new caBIG****®**** API is generated to allow data exchange between the existing tool and caGrid. **** **
**Description: Involves using caCORE to create and semantically map a new caBIG****®**** compatible API to the existing API.  The caBIG****®**** API then connects to caGrid. This may or may not require a Unified Modeling Language (UML) model**** – ****it could be a field-to-field mapping activity. **

## 2: Direct Data Access(Interim Solution)

**Use Scenario: There is a desire or need to retain the legacy database, but also willingness to adopt a caBIG****®**** tool for its user interface and to facilitate connection to caGrid. **
**Description:  Data “live” in the legacy database; caBIG****®**** tool is adapted to query that database (can be dynamic or on demand).   **
**NOTE:  This may be an effective transition strategy but is not recommended as a long-term alternative.  It may be an interim step leading into the following two patterns. **

## 3: Message Broker

**Use Scenario: The existing tool already uses standardized messages, such as HL7, to facilitate dynamic information exchange between diverse tools. **** **
**Description: A “messaging hub,” such as caXchange, brokers the transfer of messages from the existing tools, feeds into a caBIG****®**** tool, and then out to caGrid.  This same concept can be used with other file formats like CSV or tab-delimited ASCII.  caAdapter facilitates mapping into caBIG****®**** standard elements. **

## 4: Data Warehouse

**Use Scenario: There is a desire or need to retain the legacy database and user interface, but there is a willingness to use a caBIG****®**** **_**tool**_** to connect to caGrid.**** **
**Description:  Data “live” in the legacy database; Extract, Transfer, and Load (ETL) techniques are used to periodically import data into the caBIG****®**** tool to serve to caGrid.  ETL techniques are designed to ensure that data are semantically harmonized.  **

## 5: Clone and Own

**Use Scenario: There is a desire or need to retain the legacy database and user interface, and willingness to use a caBIG****®**** tool **_**API**_** to connect to caGrid.**** **
**Description:  An existing caBIG****®****- compatible API is used and “copied” into the existing tool. This involves mapping legacy schema to the caBIG****®**** API.  Reusing existing caBIG****®**** CDEs is key to this effort. If there are modifications, changes, or upgrades, the center must incorporate the changes in the API.  **

## 6: Generate an API

**Use Scenario: There is a desire to retain the legacy database, and no existing caBIG****®**** API is appropriate to map from the legacy database to caGrid.  Instead, caBIG****®**** metadata descriptions and CDEs are used to generate a new API to rest on the legacy tool. **** **
**Description:  This alternative involves using the caCORE Software Development Kit’s (SDK) shared vocabularies and CDEs to construct a brand new caBIG****®****-compatible API that is mapped to the tables in the existing legacy database. **

## Variables Affecting Adapt Options

- Three variables will help determine the investment required to adapt an existing tool – as well as the possible approach that may be most appropriate.
**Characteristics of Existing Tool - **The more visibility you have about the tool, the more options there are for adaptation.** **
**Staffing, Size, Skills, & Budget - **A team with both domain and technical experts will greatly facilitate the process – technical skill sets include data modeling and curation, annotation, familiarity with data model reuse, metadata reuse, semantic integration, Java programming, and database development skills.
**Technology Environment - **The degree of control over the infrastructure and environment may affect the choice of the best adapt path.

## Preparing for the Investment of Adaptation:  Key Stakeholders

| Challenge | Issues To Address | Domain Experts |
| --- | --- | --- |
| Understanding capabilities of caBIG® tools | What tools are available
What do they do
How they can interact with each other | Research investigators
Biostatisticians
Bioinformaticists |
| Technical specifications | Compatibility with legacy systems
Changes to legacy systems
Adaptation approach
Pipeline design
Security design | Software engineers
Information technology specialists 
Bioinformaticists
 |
| Project resource planning | Labor hours required
Technology requirements
Schedule | Project managers
Software engineers
System administrators |
| Scientific impact | Cancer Center use cases
Data availability
Protecting intellectual property | Cancer Center investigators
 |

## Lesson 7 Review: See More About Design Patterns and Tools 

| Resource | Link |
| --- | --- |
| Adaptation Roadmap: Full Presentation with Scenarios – Annual Meeting 2008  | https://cabig.nci.nih.gov/2008AnnualMeeting/presentations/wednesday-june-25-2008/session-block-1/breakout-sessions/adaptation-roadmap/adaptation/at_download/presentation  |
| HL7 / BRIDG Information | http://www.bridgmodel.org 
http://www.hl7.org    |
| CTODS | https://cabig.nci.nih.gov/inventory/infrastructure/CTODS  |
| caXchange | https://cabig.nci.nih.gov/tools/LabIntegrationHub  |

## Lesson 8: Focusing on the Grid

**Lesson 8: Focusing on the Grid**

**This lesson provides a closer look at caGrid.  This topic is critical because “getting on the Grid” – sharing data and resources – is the primary objective of caBIG****®****.  **
**Learning Objectives for This Lesson:**** **
- An overview of the purpose of a grid
- What it means to be “on the Grid”
- The major components of caGrid infrastructure and tooling
- Installing caGrid software
- Understanding grid security
- A closer look at caGrid service creation and use
**Get started quickly:  **https://cabig-kc.nci.nih.gov/CaGrid/KC/ (paste link in browser)

## Accessing Grid Demos 

**Voice over slides and screencasts can be useful in orienting you to caGrid – you can visit these before or after this lesson. **
- caGrid Introduction and Demonstration (https://webmeeting.nih.gov/p94967545/) 27-minute Audio over Slides and Screencast (turn speakers on). You may also download the Power Point slides for this demonstration at https://cabig.nci.nih.gov/inventory/infrastructure/caGrid_Demo_v7JT.ppt
**caGrid consists of several. Demonstrations for three of these are provided here: **
- caGrid Core Infrastructure: Consists of the core services, APIs, and tools. Introduce Demonstration (http://software.cagrid.org/introduce/docs/Introduce.mov)
- caGrid Workflow Client: Focuses on making workflows usable by the scientific community (early integration with Taverna). Taverna Use Demonstration (https://webmeeting.nih.gov/p44387759/)
- caGrid Portal: Provides a web-based application enabling discovery and interaction with services available on the caGrid infrastructure. Portal Use Demonstration (https://gforge.nci.nih.gov/docman/view.php/196/12815/caGridPortal.mov)
**Access a Brochure about caGrid (****https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/caGrid_brochure.pdf) **

## Grid OverviewWhat is a Grid?

**Grid Overview****What is a Grid?**

- Grids provide the infrastructure for 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.)
- Public, freely reusable (open) standards

*“**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.*

**Notes:**
Source: caGrid 1.0 Tutorial Overview

## Grid Overview What is caGrid? 

- The caGrid project provides the core software infrastructure and tooling needed to share well-defined data and resources. Its development is supervised by the caBIG® Architecture Workspace.
- caGrid and Gold Compliant tools create the *G* in caBI*G**®.*
- Connecting interoperable services and data sources to the Grid is the ultimate target of the compatibility process.** **
**HOWEVER, Gold-level compatibility involves more than Grid-enabling your tool.**  Additional requirements include CDE re-use, usage of vocabulary standards, and model harmonization.
- “Getting a service on the Grid” means creating a service which meets interoperability standards, and then connecting that service or data source to a Grid (internal or external).  Aspects of the standards include interfaces, methods, and security. Services are advertised on an index service, allowing others to find them.

## Grid Services

**What kinds of Grid services are there? **
- An **Analytical Service** executes specific calculations on a data set.  An example would be a hierarchical clustering service for microarray gene expression data.
- A **Data Service** provides access to stored information, e.g. experimental or clinical results.  In addition to meeting basic service requirements, these must implement a standard query operation and language, and expose standardized service metadata (descriptions of the data). An example would be query and retrieval of microarray data from caArray.
**What kinds of advantages will Grid services provide?  **
- Grid services are intended to allow data located in different institutions to be made easily available in standard formats.  This could afford greater statistical power to a study by collecting more samples/experiments for analysis.  It may allow joint analysis of different types of data.  For example, queries might join clinical annotations from caTissue Core with genetic association data from caGWAS.*  *Analytical services provide access to sophisticated calculations independent of any particular software package.

## Physical View of a Grid Node

- To understand “getting on the grid,” let’s look inside a grid node.
- The “grid service” provides access to a database or performs a calculation.
- The surrounding layers – the grid software – provide a standard way of exchanging information.

**Notes:**
From “caGrid Demo”  Daniela Smith

## Key Requirements

**To fully Grid-enable a system (expose a compatible tool on the Grid) one must: **
- Use **strongly typed objects** belonging to **information models** registered in the Cancer Data Standards Repository (caDSR).
- Develop **object-oriented** **APIs** to access **data resources**.
- Create a **Grid service interface** over the object-oriented APIs that defines the functionality that you are exposing to the Grid. This grid service interface uses the same strongly typed objects as your existing system, but represents them in a way that is platform and language neutral (using XML) based on registered schemas.
- Complete the 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 caBIG®-compatible tool means much of the work has already been done for you, while adapting your own tool or resource to caGrid takes more effort.

**Notes:**
Source: adapted from caGrid 1.0 Tutorial Overview, with updates from “caGrid Demo” (Daniela Smith).

## 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).**

**Notes:**
Source: Modified from caGrid 1.0 Tutorial Overview

## Advertising and Discovering Services

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

**Notes:**
Source:  caGrid 1.2 Users Guide, Figure 4-2, pg. 38

## Key Features of the Data Infrastructure

**The key to interoperability is well-defined, reusable data objects:**
- Client and service APIs are object oriented, and operate over well-defined and curated data types.
- Objects are defined in Unified Modeling Language (UML) and converted into ISO/IEC 11179 Administered Components.  These components are in turn registered in the Cancer Data Standards Repository (caDSR) to promote reuse.
- Object definitions draw from controlled terminology and vocabulary registered in the Enterprise Vocabulary Services (EVS), and their relationships are thus semantically described – they are described unambiguously.
- XML serialization of objects (for data exchange) adheres to XML schemas registered in the Global Model Exchange (GME).  The GME is used operationally on the grid, whereas the caDSR is oriented toward design and discovery.

**Notes:**
Source: modified from caGrid 1.0 Tutorial Overview.  See also caGrid 1.2 Users Guide, Figure 4-1, pg 36

## caGrid Infrastructure and ToolingThe Full Grid Environment

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

**Notes:**
Source:  www.cagrid.org

## caGrid Infrastructure and ToolingTechnology Overview

**caGrid leverages the following key technologies:**

| 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 | NCI CBIIT |
| Enterprise Vocabulary Services (EVS) | Provides controlled vocabularies | NCI CBIIT |
| 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  |
| Central Authentication Service  | Provides underlying core single sign-on framework used by WebSSO  | JA-SIG  |
| Taverna  | Provides an open source workflow tool for designing and executing workflows  | The Open Middleware Infrastructure Institute (UK)  |

## caGrid Installation Installing caGrid

- The caGrid 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 prerequisites and instructions are available online at:** **http://www.cagrid.org/mwiki/index.php?title=CaGrid:Software
- 		and
- 	https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/
- caGrid software requires that an appropriate version of Java be installed on the target machine (currently Java 1.5 JDK).   Java distributions can be downloaded from http://java.sun.com.

## caGrid SecurityWhat about Security?! 

- Some grid services, for example those dealing with clinical data, may require a strong security framework.  caGrid uses the GAARDS security infrastructure (see www.gaards.org) to provide security services.  Components include**:**
**Dorian** – Allows institutions to locally authenticate their users onto caGrid
**GridGrouper** – Manages group memberships and project access rights
**Grid Trust Services **–** **Specify which institutions trust each other’s authentication
**Authentication Service** – Integrates existing credential providers to the Grid
**Credential Delegation Services** – Provide ability to delegate credentials to other services/users
**Web Single Sign-On** – Provides single sign-on capability for Web-based applications which interact with the Grid.
**Common Security Module** – Supports the enforcement of local data access control based on group membership.
- GAARDS was developed on top of the Globus Toolkit and extends the Grid Security Infrastructure (GSI)
- The following figures show how this all fits together to form the security architecture.

**Notes:**
With updates from “caGrid Demo”.

## caGrid SecuritycaGrid GAARDS Security

- A grid application uses the GAARDS security system to:
- Authenticate the user.
- Obtain valid grid credentials.
- Potentially delegate those credentials to a remote grid service, or use them directly.
- The grid service validates the credentials, and may further check them against access control policies.

**Notes:**
Diagram Source: cagrid.org – GAARDS.  See also caGrid 1.2 Users Guide, Figure 5-1, pg 46.

## caGrid Security Grid Trust Service – Detail

- Here, the local institution’s authentication system (for example, the local network account username/password) is used to verify the identity of the user.
- The Grid Trust Service is used to indicate that this local authentication can be accepted as valid for issuing Grid credentials.
- Grid accounts can also be maintained independent of local institutions by storing them directly in a caGrid Dorian server.

**Notes:**
Source: caGrid 1.2 Users Guide Figure 5-20, pg. 80

## Grid Service Creation Creating a Grid Service

- You may wish to adapt your own data service to the Grid.
- 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 have generated public APIs for your service, the Introduce Toolkit supports the next step. Introduce is a graphical development environment, and is installed as part of caGrid.
- 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, either directly or from within Introduce.
- If the SDK is not used, you can also provide your own XML schema.
- 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.)**

## Grid Service Creation caGrid Service Layers

- We have already seen a simple view of a Grid service.  This figure shows in more detail the components that are needed manage the Grid interactions**.**** **

**Notes:**
Source: caGrid 1.0 Tutorial Overview

## Grid Service Creation Introduce – Capabilities

- The “Introduce Toolkit”, which includes a graphical wizard, greatly simplifies configuring all of these components to create your service. Here is a partial list of its 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

## Grid Service Creation 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 caBIG****®**** Grid service, configured to provide:**** **
- Advertisement
- Standard Metadata
- Security
- Complete Client API
**Graphical Deployment of Service to:**
- Tomcat
- JBoss

**Notes:**
Source: caGrid 1.0 Tutorial Overview, with added text from “caGrid Demo”.

## Grid Service Creation Introduce – Final Notes on Services & APIs

**Predefined vs. dynamic query interfaces –**
- caGrid services typically provide a client API (in the form of a Java “jar” file).  This is incorporated into the program that is used to query the Grid service and is “bound” to the particular service of interest at runtime.
- caGrid also makes it possible to dynamically invoke services for which a client program has no specific APIs.  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 specific client API 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 mechanisms to describe service invocations using a workflow language (Taverna, BPEL), and request that the workflow service perform the invocation.
- Further details on the workflow infrastructure can be found in the caGrid Programmer’s Guide.

**Notes:**
Source: based on caGrid 1.2 User’s Guide, pgs. 41

## Building Out the Grid Overview

- The preceding survey details the breadth of technologies involved in caGrid.  The following section will add detail on:
- What institutional support might be involved in actually “getting on the Grid”
- Tools already available on the Grid
- The caGrid Portal, which allows examining data in caGrid at the highest level
- The use of workflows in caGrid to automate complex processes

## Building Out the Grid Deployment and Development Requirements

**Deploying caGrid will require technology support:**
**Deploying an existing caGrid service (adoption):**
- System administrator with Web application server experience, including experience in IT security, basic understanding of digital certificate concepts and group-based authorization concepts.
**Adapting your existing data service to caGrid (adaptation):**
- In addition to the requirements for deploying a service (above), you will need a developer experienced with current Web application server development technologies.
- Establishing a new Grid application will require effort in modeling your service, e.g. using UML, and filling out code in the framework created by Introduce. The Introduce toolkit greatly simplifies the work that needs to be done in creating the basic framework.
- Completion of the full Silver or Gold compatibility process for a new service will require significant attention.

## Building Out the Grid caGrid Portal

**The caGrid Portal (http://cagrid-portal.nci.nih.gov/) allows you to use a Web browser to directly find and access available caGrid services.**
- Find and determine the status of
- 	remote services (service discovery)
- Inspect data models used by the
- 	Grid services (service metadata)
- Perform simple or complex data
- 	queries (data service query)
- caGrid account registration
- News and events

## Building Out the Grid Workflows on caGrid

- A workflow automates the steps in a complex procedure. It is particularly useful for lengthy or repetitive operations.
- caGrid is developing support for two types of workflows, Active BPEL and Taverna.  Both allow for retrieving data from Grid data services and performing calculations using Grid analytical services.
**Active BPEL **– this is an industrial-grade workflow language.
**Taverna** – a caGrid plug-in has been developed that allows workflows developed in the Taverna graphical workbench to call caGrid services.  Its goal is to simplify workflow creation.

## Building Out the Grid Workflows: caGrid Plug-in for Taverna

**Taverna caGrid “Scavenger” with semantic/metadata-based caGrid service query.**

**Notes:**
Source: caBIG 2008 Annual Meeting presentation, Workflow Working Group Presentation, Kiran Keshav et al. (Wednesday Session 3).
“caGrid Scavenger with semantic/metadata based caGrid service query”.  See also caGrid Users Guide, Chapter 6, Workflow Services.

The GT4 plug-in support semantic based service query. Users can input multiple (up to three, in current scenario three is enough. We can add more in our program upon request) service query criteria and input the corresponding value.
We can combine multiple criteria. The initial GUI only shows one query criteria, but more can be added by clicking “Add Service Query” button. For example, we can query the caGrid services whose “Research Center” name is “Ohio State University”, with Service Name “DICOMDataService”, and has operation “PullOp”.

## Lesson 8 Review: Resources

| Resource | Link |
| --- | --- |
| caGrid Knowledge Center | https://cabig-kc.nci.nih.gov/CaGrid/KC/ – Main page (paste link in browser) |
| caGrid Portal | http://cagrid-portal.nci.nih.gov/ – The Web interface to caGrid, allowing browsing for available services and inspecting service details |
| caGrid Project Web Sites
 | http://cagrid.org – Primary development site 
https://cabig.nci.nih.gov/workspaces/Architecture/caGrid - caGrid product Web site |
| caGrid User Forums and Mailing List
 | https://cabig-kc.nci.nih.gov/CaGrid/forums – Discussion forum (new)
https://list.nih.gov/archives/cagrid_users-l.html – User discussion list |
| Article about caGrid in Bioinformatics, 2006 - Saltz et al., “caGrid: design and implementation....” Bioinformatics 2006 22(15):1910-1916           | http://bioinformatics.oxfordjournals.org/cgi/content/full/22/15/1910 |

## Lesson 9:  Getting Support from caBIG® and Next Steps

**Lesson 9:  Getting Support from caBIG****®**** and Next Steps**

**This training program has: **
- Described the caBIG® initiative and its goals
- Pointed to the location of caBIG® software tools and described their benefits
- Explained the roles of interoperability, caGrid, and data sharing in achieving caBIG® goals
- Described specific actions that your organization can take to connect with caBIG®, including adopting caBIG® tools and adapting your own tools to become caBIG®-compatible
**This final lesson points you to more information ****and caBIG****®**** support resources.  **

## Understanding the Role of Knowledge Centers

**Understanding the Role of ****Knowledge Centers**

- NCI-supported organizations that provide domain-specific expertise within the caBIG® community and serve as points of contact for education,
- outreach, training, and deployment needs to the community.
**caBIG****®**** Knowledge Centers offer:              **
- Domain expertise via dynamic, interactive Web-based environment and technical and end-user documentation
- Comprehensive and up-to-date installation packages for caBIG® tools
- Administration of open source development of caBIG® tools by the community
- Collection and monitoring of defect reports, feature requests, and end-user requirements
- Access to training materials
- Searchable caBIG® knowledge base to find solutions to real-world biomedical research problems

## Understanding the Support Offered by Knowledge Centers

- Knowledge Center support consists of Web-based interaction allowing for education, outreach, training, and deployment needs through the use of:
- MediaWiki
- Web Forums
- Bug Tracking System
- Repository of Knowledge Center Development Code, Documentation, Policies, and Standards
*A visitor can browse all the resources across Knowledge Centers without an account. To edit wiki pages, add forum postings, report defects and bug requests, and download tool code, visitors will need to register for an account. Once registered, a user’s login and password can be used to provide access to all Knowledge Centers.*

## caBIG® Knowledge CentersWiki Pages

| Knowledge Center | Organization | URL (Paste link in browser) |
| --- | --- | --- |
| caGrid | The Ohio State University and The Ohio State Comprehensive Cancer Center, with the University of Chicago and the Argonne National Laboratory | https://cabig-kc.nci.nih.gov/CaGrid/KC |
| Clinical Trials Management Systems | Duke University Comprehensive Cancer Center, with Robert H. Lurie Comprehensive Cancer Center at Northwestern University, Cancer and Leukemia Group B-Information Systems (CALGB-IS), and SemanticBits | https://cabig-kc.nci.nih.gov/CTMS/KC |
| Molecular Analysis | Columbia University Herbert Irving Comprehensive Cancer Center with the Broad Institute of MIT and Harvard  | https://cabig-kc.nci.nih.gov/Molecular/KC |
| Tissue/Biospecimen Banking and Technology Tools  | Siteman Cancer Center, Washington University at St. Louis  | https://cabig-kc.nci.nih.gov/Biospecimen/KC |
| Data Sharing and Intellectual Capital | University of Michigan | https://cabig-kc.nci.nih.gov/DSIC/KC |
| Vocabulary | Mayo Clinic with SemanticBits  | https://cabig-kc.nci.nih.gov/Vocab/KC |

## Post Your Questions in theKnowledge Center Forums!

**Knowledge Center forums are available for each tool supported by the Center – Here’s the End User Forum for caTissue.  Access Forums at  ****https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Knowledge_Center_Forum_Index **

## Defining caBIG® Support Service Providers

**Support Service Providers:**
- Are NCI-licensed third-party organizations that deliver support to end users and IT professionals
- Are designated by caBIG® to ensure they provide high-quality, up-to-date and effective support for caBIG® technologies
- Provide a variety of services that may include software application and IT infrastructure support, development, and implementation
- Work with clients on a fee-for-service basis
**Current caBIG****®**** Support Service Providers cover four areas: **
- Help Desk support
- Adaptation and enhancement of caBIG®-compatible software applications
- Deployment support for caBIG® software applications
- Documentation and training materials and services

## What a Support Service Provider License Means... 

- The Service Provider Announcement was not a procurement, and no funds will be awarded to successful applicants
- caBIG® Support Service Providers are independent entities that are approved by NCI as meeting specific criteria for performance
- Actual services are rendered by caBIG® Support Service Providers to their clients under separate business arrangements organized by and between those parties only on a fee-for-service basis
- NCI Designation does not constitute an endorsement of the Support Service Provider’s business by NCI; the designation serves merely as an indication that the Provider has successfully complied with the evaluation criteria
- NCI is in the midst of license negotiations with Support Service Providers.  For a complete list, please visit https://cabig.nci.nih.gov/esn/service_providers
- Information on licensed Support Service Providers will be shared – see weekly newsletter *What’s BIG This Week* or Announce Listserv for updates

## Understanding the Boundaries: Side-by-Side Examples

| Knowledge Centers | Support Service Providers |
| --- | --- |
| Provide Web-based support  | Define support by client-specific agreements/contracts  |
| Make minor enhancements and bug fixes to existing software based on workspace priorities  | Perform specialized development based on workspace and end-user needs |
| Foster open development across community | Customize applications to meet individual user needs |
| Serve as steward of caBIG® software code base | Create “shrink wrap” full-featured applications from caBIG®-funded reference implementations |
| Maintain and update tool outreach materials, documentation, and training materials | Customize documentation and training for specific clients/end users based on their needs |

## Using the ESN: A Case Study 

**A Principal Investigator (PI) considers deploying a biospecimen repository...**** **
- Based on interest from investigators at her institution, the PI consults the caBIG® Web site and finds information about the Tissue/Biospecimen Banking Tools Knowledge Center
- The PI visits the Knowledge Center Web site, discovers that caTissue fulfills her needs, and downloads software and associated documentation from the site
- The PI contacts a caBIG® Support Service Provider and contracts for assistance with installation and data migration
- After using caTissue for several months, the PI desires additional functionality and posts her ideas in the Knowledge Center user forum
- The Knowledge Center brings her ideas to the Tissue Banks and Pathology Tools Workspace, where needs are identified and priorities set
- Given the specialized nature of her needs, the PI chooses to negotiate with a caBIG® Support Service Provider for custom enhancements

## For More About caBIG®

| Resource | Link |
| --- | --- |
| The caBIG® Web site is the best centralized resource for general caBIG® information  | https://cabig.nci.nih.gov/  |
| Access caBIG® tool demos and information through a searchable database | https://cabig.nci.nih.gov/tools/toolsuite_view  |
| To send in a specific question about caBIG®, write to this e-mail  | caBIGconnect@cancer.gov  |
| Read postings to the “caBIG® Announce Listserv” where community news and notices are posted | https://list.nih.gov/archives/cabig_announce.html  |
| Contact NCICB Applications Support for technical help with NCICB applications and tools  | ncicb@pop.nci.nih.gov  |

## Training Credits

**This training was developed by the caBIG****®**** Documentation and Training Workspace.  Special thanks go to: **
- Jessica Bondy – University of Colorado
- Bart Brown and Tom Casavant – Holden Comprehensive Cancer Center at the University of Iowa
- Robert Freimuth – Mayo Clinic Comprehensive Cancer Center
- 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
**D&T Workspace Leads: Leslie Derr (NCI CBIIT) & Jennifer Tucker ****(OKA – Otto Kroeger Associates)**