caBIG™ Essentials: Self-Paced Training Program . Prepared by the caBIG™ Documentation and Training (D&T) Workspace – Last Updated: 8 November 2007 . Getting Started: Click on right arrow below to advance to the next slide. Training Overview:. Training Topic, Audience & Prerequisites.
caBIG™ Essentials: Self-Paced Training Program Prepared by the caBIG™ Documentation and Training (D&T) Workspace – Last Updated: 8 November 2007 Getting Started: Click on right arrow below to advance to the next slide.
Training Overview: Training Topic, Audience & Prerequisites • Topic Statement: This training provides an overview of the caBIG™ program and its offerings. 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 connect with 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™. Those familiar with caBIG™ may wish to skip material in Lesson 1, and proceed to later lessons.
Training Overview: Lesson Plan • Lesson 1: Introduction to caBIG • Lesson 2: caBIG™ Self-Assessment & Tools Overview • Lesson 3: Focus on Clinical Trials Compatibility Framework • Lesson 4: Focus on Life Sciences Distribution • Lesson 5: Making A Tool caBIG™ Compatible – Overview • Lesson 6: Focus on the Grid • Lesson 7: Focus on caBIG™ Data Sharing and Security Framework • Lesson 8: Conclusion
Training Overview: Training Program Goals • By the end of this training, you will be able to: • Describe the caBIG™ initiative and its goals. • Locate caBIG™ software tools, so that you can evaluate their benefits against your needs, and determine their appropriateness for implementation in your organization’s environment. • Explain the roles of interoperability, the Grid, and data sharing in achieving caBIG™ goals. • Evaluate and select specific actions that your organization can take to connect with caBIG™, including adopting caBIG™ tools and adapting your own tools to become caBIG™ compatible.
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™ Structure and Organization • Introduce Key caBIG™ Concepts • Explain What it Means to Connect with caBIG™ • Determine Your Path Forward • Decide Where to Go Next in This Training
Lesson 1: Introduction to caBIG™ caBIG™ and Its Goals • Launched in 2004, the cancer Biomedical Informatics Grid (caBIG™) is an information technology program that is redefining how cancer research is conducted. • The vision of caBIG™ is a full cycle of integrated cancer research, extending from bench to bedside, and back again. • We do this by: • Developing software tools that support cancer research efforts, and by • Establishing a common infrastructure that can be used to share data and applications across organizations.
Lesson 1: Introduction to caBIG™ caBIG™ and Its Goals • The Goals of caBIG™ are to: • Connect cancer research communities through a shareable and interoperable infrastructure • Develop standard rules and a common language to more easily share information • Build or adapt tools for collecting, analyzing, integrating, and disseminating information associated with cancer research This training program is designed for people who want to support caBIG™ goals by adopting caBIG™ tools, applying the standards that support data sharing with others in the caBIG™ community, and connecting to the caBIG™ infrastructure. If your interest in caBIG™ is more general, please visit the caBIG™ Public Website: http://cabig.cancer.gov – Note: all links in this training open a new window/tab!
Lesson 1: Introduction to caBIG™ How Connecting with caBIG™ Benefits You • Connecting with caBIG™ benefits cancer research organizations in the following ways: • 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 to others. • The increased data sharing made possible by connecting with caBIG™ increases the effectiveness and efficiency of cancer research, helping individual scientists, the cancer research community, and – ultimately - patients.
caBIG™: From Pilot to Enterprise Lesson 1: Introduction to caBIG™ caBIG™ began with the vision of creating a virtual web of interconnected data, individuals, and organizations that redefines how research is conducted, care is provided, and patients/participants interact with the research enterprise 2004 – 2006 • PILOT PHASE • 1,000 individuals from over 190 organizations • Developed a standards-based caGrid infrastructure • 40 applications that support basic/ clinical cancer research 2007 • ENTERPRISE PHASE • Rollout of available caBIG™ tools and infrastructure to • NCI-designated Cancer Centers • Formation of an enterprise support network • Engagement with the broader biomedical research community
Lesson 1: Introduction to caBIG™ caBIG™ Structure and Organization • 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. • Many caBIG™ activities are carried out in management structures called workspaces. • Domain workspaces focus on specific areas of cancer research, and oversee the development of domain-focused software tools. • Cross-cutting and Strategic workspaces support these groups by developing standards, infrastructure, policies, and documentation. • The following slides introduces these workspaces and their missions.
Lesson 1: Introduction to caBIG™ What it Means to Connect with caBIG™ • There are two basic ways to become connected with caBIG™: • Adopt a caBIG™ Tool and then Connect to the Grid: You can connect with caBIG™ by adopting pre-existing caBIG™ compatible tools and then connecting through caGrid. This is best if you need domain-specific tools, caBIG™ has tools that meet these needs, and you are prepared to install the caBIG™ tools and integrate them into your workflow. • Adapt a Tool to make it caBIG™ Compatible and then Connect to the Grid: If you have a tool (either created in-house or by a vendor) that is not caBIG™ compatible, you can achieve compatibility by reengineering the existing tool or creating an interface that maps an existing tool’s data structures and APIs to caBIG™ standards. Once the tool is compatible, you can connect to the Grid. • The following sequence of diagrams shows how these options play out – ultimately aligning with the key concepts just covered.
Pathways to caBIG™ Compatibility Lesson 1: Introduction to caBIG™ ADOPT ADAPT Available caBIG™ Applications There are many existing caBIG™ compatible applications that can be adopted and then connected to the Grid with ease. Lessons 2-4 introduce these tools. App 2 App 1 caGrid
Pathways to caBIG™ Compatibility Lesson 1: Introduction to caBIG™ ADOPT ADAPT Available caBIG™ Applications App 2 App 1 Connecting a caBIG™ compatible application to the Grid (creating a Grid node) is facilitated by caBIG™ tools and infrastructure – Lesson 6 addresses this process in more depth. caGrid
Pathways to caBIG™ Compatibility Lesson 1: Introduction to caBIG™ ADAPT ADOPT ADAPT Available caBIG™ Applications Existing Applications App 2 App 4 App 1 App 3 You can also adapt your own tool to be caBIG™ compatible and then connect to the Grid – this is generally more labor intensive than adopting a tool, and will require support from a development team with certain skills and experience. We discuss this in Lessons 5 and 6. caGrid
Pathways to caBIG™ Compatibility Lesson 1: Introduction to caBIG™ ADAPT ADOPT ADAPT Available caBIG™ Applications Existing Applications You do not need to make the entire application compatible to connect to the Grid – just the elements that you wish to expose. Once compatibility is achieved, connecting to the Grid is facilitated by caBIG™ tools and infrastructure – Lessons 5 and 6 address these processes in more depth. App 2 App 4 App 1 App 3 caGrid
Pathways to caBIG™ Compatibility Lesson 1: Introduction to caBIG™ ADAPT ADOPT ADAPT Available caBIG™ Applications Existing Applications App 2 App 4 App 1 App 3 caGrid
Lesson 1: Introduction to caBIG™ Life on the Grid: Implementation Scenarios
ADOPTING MAY BE BEST IF… You have requirements that caBIG™ tools can fulfill in the domains of clinical trials, bench research, imaging, and/or tissue banking. End users are open to learning new tools and integrating them in their workflow. You do not have a technical team available to build or reengineer software, but you can to leverage internal resources to support a software installation effort. ADAPTING MAY BE BEST IF… You have existing technology infrastructure and tools that meet the needs of the users, and that are already integrated into workflows. You have technical team(s) available with (1) software development expertise, particularly in the areas of data modeling and application programming interface (API) development. (2) Previous experience with the NCI’s vocabulary and data model tools/repositories. Lesson 1: Introduction to caBIG™ Determining the Best Path for You To learn about this path, you may want to focus on Lessons 2, 3 and 4 To learn about this path, you may want to focus on Lessons 5 and 6
Lesson 1: Introduction to caBIG™ Determining the Best Path for You • While “adopt or adapt” are the two basic ways to connect with caBIG™, hybrid approaches exist. Here are two examples: • Integrate a caBIG™ module within your existing bioinformatics infrastructure, and develop an interface to facilitate data exchange between them. • Create a caBIG™-compatible “wrapper” around an existing tool, so that data appropriate for external data sharing can be more easily served, while not reengineering an entire tool. • Which options are best for your organization? The rest of this training program will help you determine the best choices based on your existing needs, infrastructure, and capability.
Lesson 1: Introduction to caBIG™ Decide Where to Go Next in This Training • Here’s some tips on what to explore next in this training:
Lesson 1: Introduction to caBIG™ Lesson Review • In this lesson, we: • Discussed the goals of caBIG™ and the benefits of getting connected. • Reviewed key concepts and terms related to the caBIG™ effort. • Introduced different methods of getting connected with caBIG™, including adopting caBIG™ tools and adapting existing tools. • The next three lessons will focus on the different tools available from caBIG™ - these focus on connecting with caBIG™ through tools adoption.
Lesson 2: caBIG™ Self-Assessment & Tools Overview • This lesson begins by pointing to a self-assessment to help identify your readiness to connect with caBIG™. Then, we introduce you to the full range of tools available from caBIG™. While some organizations will adopt groupings of tools called bundles, others may want to adopt individual tools independent of those bundles. This lesson will also introduce you to the infrastructure offered by caBIG™. • Learning Objectives for this Lesson: • Point to a caBIG™ Self-assessment • Point you to a comprehensive list of caBIG™ tools • Introduce key elements of the caBIG™ Infrastructure • Introduce the “Bundles” concept
Lesson 2: caBIG™ Self-Assessment & Tools Starting with a Self-Assessment • Getting started with caBIG™ involves three key steps: • Assess where you are – What tools and infrastructure does your organization already have? What’s your level of readiness to engage with caBIG™? Want a systematic set of questions to define your starting state? Review caBIG™ Deployment Self-Assessment (PDF). • Determine where you want to be – Where are the gaps that caBIG™ may be able to fill? • Build a plan for getting there – Decide what you will adopt and adapt, and how you will engage with the Grid. • Understanding what’s available can help you determine where you are and where you want to go – the rest of this lesson will point you to the tools and infrastructure already available through caBIG™.
Web Object Placeholder Address:https://cabig.nci.nih.gov/tools/ Displayed in: Articulate Player Window size:320 X 240 Lesson 2: caBIG™ Self-Assessment & Tools caBIG™ Website Tools Landing Pages • Tools pages on caBIG™ website provide a full listing of caBIG™ tools – with information to support their use - Visit https://cabig.nci.nih.gov/tools/
Web Object Placeholder Address:https://cabig.nci.nih.gov/inventory/Infrastructure/ Displayed in: Articulate Player Window size:600 X 240 Lesson 2: caBIG™ Self-Assessment & Tools A Look at the caBIG™ Infrastructure • caGrid (The Grid) and caCORE are two vital resources when connecting with caBIG™. We’ll talk more about these later, but visit https://cabig.nci.nih.gov/inventory/Infrastructure/ to preview the caBIG™ infrastructure – the backbone of caBIG™.
Lesson 2: caBIG™ Self-Assessment & Tools A Starting List of Candidate Tools • To help audiences identify related tools more easily, 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, which can interoperate or be used in workflows through the caGrid infrastructure. A third bundle deals with data sharing and compatibility policies. • Example tools from the three bundles are listed on the next slide: • Clinical Trials Compatibility Framework • Life Sciences Distribution • Data Sharing and Security Framework
Compatibility Achieved through caBIG™ Bundles Lesson 2: caBIG™ Self-Assessment & Tools Introducing the Bundles Clinical Trials Compatibility Framework Data Sharing and Security Framework Life Sciences Distribution • CTODS • caArray • caTissue • geWorkbench • caGWAS • NCIA • caGrid • C3PR • PSC • caAERS • caXchange • CTODS • caGrid • caBIG™ Policies • Processes and Best Practices • Model Documents • Trust Fabric More in Lesson 4! More in Lesson 7! More in Lesson 3!
Lesson 2: caBIG™ Self-Assessment & Tools Lesson Review • In this lesson, we: • Presented the three central steps to connecting with caBIG™: Assessing where you are, deciding where you want to go, and planning to get there. • Provided links to existing tools and infrastructure provided by caBIG™ • Introduced the concept of the caBIG™ bundles to facilitate tools adoption • The next two lessons will focus more closely on the software bundles related to clinical trials and life science distribution - these focus on connecting with caBIG™ through tools adoption.
Lesson 3: Focus on the Clinical Trials Compatibility Framework • 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. • Learning Objectives for this Lesson: • Describe the Purpose of the Framework and End User Benefits • Provide an Overview of the Clinical Trials Suite and Supporting Tools • Review Success Criteria • Decision Support: Adopt, Adapt or Hybrid
Lesson 3: Clinical Trials Compatibility Framework Welcome to CTMS & Its Goals • The Clinical Trials Management Systems (CTMS) Workspace oversees the development and integration of tools for the framework. • Workspace goals include facilitating the following aspects of clinical trials: • Planning and instantiation of clinical trials (and monitoring of trials once they are instantiated) • Conduct of clinical trials • Reporting of clinical trials data to sponsors • Interoperability • Increase the ability to share data • Increase the ability to use the functionality of tools on other systems
Lesson 3: Clinical Trials Compatibility Framework Purpose of the Framework • The caBIG™ Clinical Trials Suite is an integrated, stable, and secure collection of interoperable software tools that support the management of study participant information through the clinical trial lifecycle. • The current version of the framework enables management of tasks such as: • Screening and registering patients for accrual to clinical trials; • Scheduling and tracking of patient encounters during the course of a study; • Integrating laboratory results with the patient record; • Tracking and managing adverse events; • Capturing, storing, analyzing and routing clinical data in a meaningful manner.
Lesson 3: Clinical Trials Compatibility Framework End User Benefits of the Framework • Adopting the Clinical Trials Compatibility Framework will ultimately facilitate the management of clinical trials. • The caBIG™ infrastructure supplements the software tools to support communication and security. • These tools are available at no cost to the end user – they will all be available by early 2008. • Once installed by an organization, the tools are designed to be used through a standard internet web browser.
caBIG™ Clinical Trials Compatibility Framework Architecture • caAERS: Cancer Adverse Event Reporting System • caXchange: Cancer Data Exchange System • PSC: Patient Study Calendar • C3PR: Cancer Central Clinical Participant Registry • CTODS: Clinical Trials Object Data System • caGrid: caBIG™ compatible systems architecture PSC caXchange caAERS C3PR CTODS CLINICAL TRIALS COMPATIBILITY FRAMEWORK Data Sharing & Security Framework caGrid Data for Sharing
Lesson 3: Clinical Trials Compatibility Framework Cancer Adverse Event Reporting System (caAERS) • Cancer Adverse Event Reporting System (caAERS) – Captures and manages reports describing adverse events that occur during clinical trials. • Allows the collection, management and querying of adverse event data (both routine and serious) • Provides configurable rules to facilitate management and reporting of adverse events at protocol, sponsor and institution levels • Generates customizable reports and submits to external agencies, including generation of NCI and FDA compliant reports. • Supports regulatory compliance • Maps to vocabularies and coding systems Click Here to Visit caAERS Tools Page Click above and a new browser tab or window will appear.
Lesson 3: Clinical Trials Compatibility Framework caXchange • caXchange - Facilitates the automatic capture of data from clinical systems and then performs an automatic translation and import to caBIG™ compatible clinical trials databases. • Enables automatic transfer of clinical data from point-of-care systems in medical centers, such as clinical chemistry lab systems. • Incorporates caXchange Lab Viewer, allowing viewing of clinical lab data imported from clinical chemistry and other lab systems. • Labs can be selected for loading into clinical trials databases and/or adverse event reporting systems • Automatically flags lab values that may indicate toxicities Click Here to Visit caXchange Tools Page Click above and a new browser tab or window will appear.
Lesson 3: Clinical Trials Compatibility Framework Patient Study Calendar (PSC) • Patient Study Calendar (PSC) - Enables clinical trial managers to schedule and manage treatment and care events for participants in a clinical trial. • Accommodates interventional, epidemiological (and population), and observational studies. • Represents study workflow in time, process, and phases • Represents event-driven and date-driven behaviors • Allows creation, editing, and management of study calendar templates over the lifecycle of a study • Allows retrospective outcomes review and reporting of calendar activities • Tracks activities as they occur and provides a framework for reviewing historic study calendar events • Provides consent / re-consent notification and tracking Click Here to Visit PSC Tools Page Click above and a new browser tab or window will appear.
Lesson 3: Clinical Trials Compatibility Framework Cancer Central Clinical Participant Registry (C3PR) • Cancer Central Clinical Participant Registry (C3PR) - Tracks subject registrations to clinical trials. • Provides repository for participant information across studies, sites, systems, and organizations as well as current enrollment statistics • Verifies registration criteria (study open, participant eligible, consent received) • Facilitates Summary 3 & 4 reporting, by providing extracts of data elements needed for these reports • Manages study personnel who have access to the registry • Facilitates compliance with Federal regulations including 21 CFR Part 11, HIPAA and Section 508 Click Here to Visit C3PR Tools Page Click above and a new browser tab or window will appear.
Lesson 3: Clinical Trials Compatibility Framework Clinical Trials Object Data System (CTODS) • Clinical Trials Object Data System (CTODS) - Enables storing and sharing of clinical trials data in both identifiable and de-identified form. • Enables data from any Clinical Trials Data Management System (CDMS) or data source to be available to the cancer research community • Provides the broader cancer research community with de-identified clinical trials data (data that have all patient identification information removed) • Consistent with the Biomedical Research Integrated Domain Group (BRIDG) model that underpins data interchange standards and technology solutions, which enable harmonization between the biomedical/clinical research and healthcare arenas. • Note: CTODS was also previously known as CTOM (Clinical Trials Object Model).
Lesson 3: Clinical Trials Compatibility Framework Integration and Interoperability Tools • A vital part of the framework consists of the tools and infrastructure that help you connect local clinical trials data management investments to the caBIG™ network. • caGrid - caBIG™-compatible systems architecture • Clinical Data Management System (CDMS) Integration • These also provide security features and access controls to ensure protection of human subject information and clinical research data. • These are covered further on the following two slides.
Lesson 3: Clinical Trials Compatibility Framework caGrid • caGrid provides the services backbone for data and message exchange across all the tools. • Connects all the tools in the caBIG Clinical Trials Framework • Provides common identity and security management across the tools • Facilitates message transport and routing between systems • Manages secure access, query and retrieval of data across tools • Contains an index of registered services • caGrid is the topic of Lesson 6. Click Here to Visit caGrid Page Click above and a new browser tab or window will appear.
Lesson 3: Clinical Trials Compatibility Framework CDMS Integration • Clinical Data Management System (CDMS) Integration enables the exchange of data between the framework tools and a caBIG™ compatible clinical data management system. • Data retrieval from CDMS products that use the caBIG Common Data Elements (CDE’s) and standard Case Report Forms (CRF’s) • Supports conforming CDMS products, such as Cancer Central Clinical Database (C3D) • Reduces data entry errors and facilitates clinical trials workflows
Lesson 3: Clinical Trials Compatibility Framework Installation and Infrastructure Basics • The caBIG™ Clinical Trials Framework is a series of enterprise applications that must be installed in a sufficiently robust computer server environment. • Examples of the dependent software that may be required include: • Apache Ant, Maven, Service Mix, Tomcat • Java SE Development Kit (JDK) • MySQL Database, Oracle Database or PostGreSQL Database • caBIG-compatible Clinical Data Management System (CDMS)
Lesson 3: Clinical Trials Compatibility Framework Adoption Success Criteria • Successful adoption of the 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: Clinical Trials Compatibility Framework Decision Support: Adopt, Adapt or Hybrid • Each organization’s circumstances and environment will be unique. • The caBIG™ Deployment Self-Assessment can help decide whether the path to caBIG™ compatibility lies in: • Adoption of the full caBIG™ Clinical Trials Suite • Adaptation of existing systems to connect to the Grid. • Use a Hybrid approach to facilitate the bridging of existing, non-caBIG™ systems to the caBIG™ infrastructure. • Organizations can choose which of these paths, or which combination of these paths, best serves their needs.
Lesson Review Lesson 3: Clinical Trials Compatibility Framework • In this lesson, we: • Presented the purpose and end benefits of the Clinical Trials Compatibility Framework • Introduced the tools and infrastructure provided by the framework • Summarized success criteria related to adopting the framework, and reminded users of the different paths towards that end See Also: Getting Connected with caBIG™ Clinical Trials Compatibility Framework (PDF)
Lesson 4: Focus on the Life Sciences Bundle • This lesson provides a closer look at the Life Sciences software bundle. • Learning Objectives for this Lesson: • Describe the Purpose of the Bundle and End User Benefits • Provide an Overview of Bundle Tools • Review Success Criteria
Lesson 4: Life Science Distribution Purpose and End User Benefits • Modern Cancer Research involves: • Complex study designs including: capture and refinement of clinical data; and selection of tissue/serum samples for molecular analysis • High-throughput molecular assays (e.g., RNA microarrays, CHiP on CHiP, Protein gels, spectrometry, SNP chips, etc) • Sophisticated analyses involving interdisciplinary teams of investigators, and advanced algorithms and software. • Integration of data and analyses (automated and human) • The Life Sciences Distribution is a set of tools and infrastructure to provide support for interdisciplinary teams engaged in translational cancer research. It supports: • Data capture and analysis • Management of clinical trial and biospecimen resources. • Sharing of data and interchange of experimental results among geographically distributed teams of interdisciplinary investigators.