National Cancer Institute Resources

Resource:Ā  National Cancer Institute - The Cancer Genome Atlas

Mission and Goal

The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.
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News from the Pilot Project

NEW Update*The Cancer Genome Atlas Reports First Results of Comprehensive Study of Brain Tumors: Large-Scale Effort Identifies New Genetic Mutations, Core Pathways
The Cancer Genome Atlas Research Network reported the first results of its large-scale, comprehensive study of the most common form of brain cancer, glioblastoma (GBM) in the Sept. 4, 2008 advance online edition of the journal Nature. Among the TCGA findings are the identification of many gene mutations involved in GBM, including three previously unrecognized mutations that occur with significant frequency; and the delineation of core pathways disrupted in this type of brain cancer. One of the most exciting results is an unexpected observation that points to a potential mechanism of resistance to a common chemotherapy drug used for brain cancer.
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TCGA Moving Molecular Oncology Forward
The Cancer Genome Atlas (TCGA) pilot project, a collaborative effort between the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), has made valuable progress as new data is continually generated and shared internationally among researchers. With new technologies and tools being developed, TCGA is enabling researchers to delve further into the molecular machinery of cancer with greater precision and efficiency.
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Reference:
National Cancer Institute. (2008). The cancer genome atlas. Retrieved October 13, 2008, from http://cancergenome.nih.gov/Ā Ā 


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Resource:Ā  National Cancer Institute - Cancer Biomedical Informatics Grid

Takeaways: CaBig Fact Sheet

caBIGā„¢ stands for the cancer Biomedical Informatics Gridā„¢. caBIGā„¢ is an information network enabling all constituencies in the cancer community – researchers, physicians, and patients – to share data and knowledge.Ā  The components of caBIGā„¢ are widely applicable beyond cancer as well.

The mission of caBIGā„¢ is to develop a truly collaborative information network that accelerates the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient outcomes.

The goals of caBIGā„¢ are to:

  • Connect scientists and practitioners 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 and care.

Since its inception, caBIGā„¢ has committed to the following cornerstones:

  • Federated: caBIGā„¢ software and resources are widely distributed, interlinked, and available to everyone in the cancer research community, but institutions maintain local control over their own resources and data.
  • Open-development: caBIGā„¢ tools and infrastructure are being developed through an open, participatory process. caBIGā„¢ leverages existing resources whenever possible, rather than building new tools in every case.
  • Open-access:caBIGā„¢ resources are freely obtainable by the cancer community to ensure broad data-sharing and collaboration.
  • Open-source: The caBIGā„¢ source code is available to view, alter, and redistribute.

 

Learn concepts and terminology critical for working with caBIGā„¢

Look up acronyms and unfamiliar terms

  • Visit the glossary: The Glossary of Acronyms and Terms has definitions for caBIGā„¢ acronyms and common bioinformatics terms.
  • View definitions as you read:. Terms in the glossary are underlined with blue dots. Roll your mouse over the term and it's definition will show. E.g., rest your mouse on this term - Domain Analysis Model

 

Frequently Asked Questions

What is caBIGā„¢?
Who are the caBIGā„¢ partners? What role do they play?
How does caBIGā„¢ work?
Industry Partners FAQs
More information and getting involved


What is caBIGā„¢?

What is caBIGā„¢?
What is the mission of caBIGā„¢?
What current needs does caBIGā„¢ address?
What are the principles guiding the work funded by caBIGā„¢?
When did caBIGā„¢ get started?
How is caBIGā„¢ organized?
How are the priorities of caBIGā„¢ established?
What are caBIGā„¢ workspaces?
What is the benefit of an interoperable infrastructure?
What is the significance of ā€˜Open Access, Open Source’ to cancer research?
What are the challenges facing caBIGā„¢?
What is the role of the NCI in caBIGā„¢?
What is NCI’s vision for caBIGā„¢?


Who are the caBIGā„¢ partners? What role do they play?

What organizations and partners currently participate in caBIGā„¢?
What are the specific constituencies in the caBIGā„¢ community and how are they involved?
What is the incentive to become a caBIGā„¢ adopter?


How does caBIGā„¢ work?

How are the activities of caBIGā„¢ structured and managed?
What are the key elements of caBIGā„¢?
Where can I find information on the grid infrastructure for the caBIGā„¢ initiative?
What is meant by ā€˜caBIGā„¢ compatibility’?
What are the current caBIGā„¢ compatibility levels?
How is caBIGā„¢ Compatibility Evaluated?
What is the status of caBIGā„¢ compatibility certification for commercial systems?
What can be said about an application that is intended to be caBIGā„¢ compatible and has been developed in compliance with the compatibility guidelines, but has not been certified?
Can a commercial application that was not created as a caBIGā„¢ application be converted into a caBIGā„¢-compatible application? If so, does the resulting application become open source?
Does any development work done by a commercial organization for a cancer center on caBIGā„¢ - funded work or directly funded through a competitive Request For Proposals (RFP) and contract become open source?
How will caBIGā„¢ ensure that data shared across centers will be secure and that the privacy of human subjects will be upheld?
Can anyone download a caBIGā„¢ application?
How is caBIGā„¢ funded?


Industry Partners FAQs

What are the benefits to commercial organizations of participating in caBIGā„¢?
Can a commercial organization take the open source software that they have developed with caBIGā„¢ funding (directly, or indirectly from a Cancer Center) and use this in existing applications? Can applications with this incorporated code be marketed and sold?
How can commercial organizations share caBIGā„¢ compatible applications with the caBIGā„¢ community?
How can commercial organizations participate in the caBIGā„¢ initiative?
Are there opportunities for commercial organizations to assist NCI with the coordination and support of the caBIGā„¢ initiative?


More Information and getting Involved

How can I learn more about caBIGā„¢?
How do I get involved with caBIGā„¢?


What is caBIGā„¢?
caBIGā„¢ stands for the cancer Biomedical Informatics Gridā„¢. It is an open-source, open-access information network enabling cancer researchers to share tools, data, applications, and technologies according to agreed-upon standards and identified needs. The goal of caBIGā„¢ is to provide an informatics infrastructure that supports a collaborative network, or ā€œgrid,ā€ among the cancer and biomedical research communities. The infrastructure and tools of caBIGā„¢ are widely applicable beyond the cancer community.

What is the mission of caBIGā„¢?
The mission of caBIGā„¢ is to promote and facilitate the following:

  • Set of common data standards
  • Sharable, interoperable infrastructure
  • Tools for applying information associated with cancer research and care
  • Data sharing among appropriate individuals and organizations, with safeguards for privacy and security

What current needs does caBIGā„¢ address?
Recent advances in cancer research methods and technologies have resulted in an explosion of information and knowledge about cancers and their treatment. The ability to characterize and understand cancer is growing exponentially on the basis of information from genetic and protein studies, clinical trials, and other research endeavors. However, the capacity to capitalize on the opportunities from these advances is limited by certain factors.
Historically, there has been no one approach to integrate the data tools used by research, the software that supports clinical trials, and the reporting tools that make sense of it all.There is no common mechanism for individual researchers, or even institutions, to easily share data. In addition, there is no unifying infrastructure or common standard for the technologies that cancer researchers currently use. This means that researchers often operate in a near vacuum, or silo approach, without benefit of information from outside their institution. They cannot easily share data or tools or benefit from the innovative technologies developed by others.
To address these issues, caBIGā„¢ is developing the components of an interoperable infrastructure.

What are the principles guiding the work funded by caBIGā„¢?
caBIGā„¢ work must be open source (caBIGā„¢ source code that is available to view, alter, and redistribute), open access (caBIGā„¢ resources that are freely obtainable), open development (caBIGā„¢ products that are developed through an open, participatory process), and federated (a caBIGā„¢ united network of systems that can be locally controlled).

When did caBIGā„¢ get started?
The caBIGā„¢ initiative was announced in July 2003 under the coordinating supervision of the National Cancer Institute (NCI) and was launched as a 3-year pilot project in February 2004.

How is caBIGā„¢ organized?
caBIGā„¢ is a partnership with the cancer community and other stakeholders. In total, nearly 50 cancer centers and 30 other organizations - over 800 people in all - are working collaboratively on caBIGā„¢.

How are the priorities of caBIGā„¢ established?
caBIGā„¢ development began with a survey of NCI-designated comprehensive cancer centers to determine their top priorities. The survey demonstrated the breadth of the needs of the oncology community - a breadth that caBIGā„¢ has been designed to accommodate. Specific caBIGā„¢ areas, or workspaces, were identified through this community input. The workspaces continue to generate priorities for the initiative, so that caBIGā„¢ can focus on the needs of the community. The priorities of the individual workspaces are expressed in workspace strategic plans, which are integrated into the caBIGā„¢ strategic plan. Additionally, the NCI identifies areas where caBIGā„¢ can contribute.

What are caBIGā„¢ workspaces?
caBIGā„¢ workspaces are areas of focus that are developing applications, policy documents, and other efforts within the caBIGā„¢ initiative. caBIGā„¢ workspaces were first identified through the caBIGā„¢ survey. They continue to be defined and developed based on continu¬ing critical input from the caBIGā„¢ community. Through the workspace networks, cancer centers provide help, develop solutions and provide data and subject matter expertise to the caBIGā„¢ community. Collectively, the workspaces are driving caBIG’s goals, priorities and activities.
Currently, the workspaces include:

  • Architecture
  • Clinical Trial Management Systems (CTMS)
  • Data Sharing and Intellectual Capi- tal (DSIC)
  • Integrative Cancer Research (ICR)
  • In Vivo Imaging
  • Strategic Planning
  • Tissue Banks and Pathology Tools (TBPT)
  • Training
  • Vocabularies and Common Data Elements (VCDE)

What is the benefit of an interoperable infrastructure?
An interoperable infrastructure will provide users the ability to share tools and data to address cancer challenges in ways not currently possible. caBIGā„¢ users can choose any number of different applications developed by different community members as well as commercial applications designed to be interoperable with caBIGā„¢, and those applications will be able to exchange information. Interoperability between computer systems from organization to organization—or even within an organization—is key to this sharing of data. Interoperability is also becoming a standard of quality in Web services.

What is the significance of ā€˜Open Access, Open Source’ to cancer research?
By applying many of the same principles that led to the popularity of free software such as the Linux operating system, the caBIGā„¢ program facilitates a cost-effective, distributed development of new tools and techniques. Thus, caBIGā„¢ components remain available to the research community as well as to other government agencies, and nonprofit and commercial organizations. Software components can be re-used in new tools, and tools can be bundled into suites of programs by other developers. As a result, continuous innovation is among the fundamental building blocks of caBIGā„¢.

What are the challenges facing caBIGā„¢?
caBIGā„¢ is addressing the challenges related to the variability of cancer research data sets and tools; the volume and complexity of cancer research data; and the lack of standards, unifying infrastructure, and mechanisms for sharing data and resources. However, while caBIGā„¢ efforts can enable and promote the sharing of information, many other stakeholders—including individual researchers—must make a commitment to information sharing and collaboration.

What is the role of the NCI in caBIGā„¢?
caBIGā„¢ is a key initiative of the NCI. As a government agency, NCI stewards caBIGā„¢ so that the needs of the entire cancer community are addressed and represented. Through its coordination, the NCI ensures that caBIGā„¢ is defined by participant cancer community members and built with their collaboration. The NCI Center for Bioinformatics (NCICB) provides active management of caBIGā„¢ and works in collaboration with partners in the public, private, and academic sectors.

What is NCI’s vision for caBIGā„¢?
NCI’s vision is that caBIGā„¢ will eventually involve the full range of the cancer research community, both nationally and internationally. caBIGā„¢ promises to accelerate progress in all aspects of cancer research - including etiologic research, prevention, early detection and treatment. NCI believes that caBIGā„¢ will help redefine how cancer research is conducted, and eventually, how cancer care is provided.


Who are the caBIGā„¢ partners? What role do they play?

What organizations and partners currently participate in caBIGā„¢?
The first group of caBIGā„¢ participants included the NCI, more than 50 of its designated cancer centers, and dozens of other organizations in the public, nonprofit, and private sectors. Because caBIGā„¢ is designed as an open-development process, other members of the cancer community and the private sector can become involved at any time. NCI welcomes new adopters of and participants in the caBIGā„¢ program. In fact, caBIGā„¢ increasingly includes participants from non-cancer communities, given the wide applicability of caBIG™’s foundational infrastructure and tools.

What are the specific constituencies in the caBIGā„¢ community and how are they involved?
The involvement of a few key caBIGā„¢ constituency groups is briefly described in the following list:

Cancer Centers

  • caBIGā„¢ was conceived, designed, and developed in partnership with the NCI-designated cancer centers. Cancer centers and volunteer teams from within their communities are involved in the development and testing of applications, tools, and other resources that are part of the ongoing design of caBIGā„¢. Cancer centers that are funded to participate in caBIGā„¢ can choose to subcontract with a vendor to undertake caBIGā„¢ project activities. These activities must comply with the principles of the caBIGā„¢ initiative: the work must be open source, open access, open development, and federated.

Individuals

  • Scientists, informaticists, and others in the cancer community who have needs addressed by caBIGā„¢ participate in the program through their involvement in workspaces, ongoing caBIGā„¢ meetings and tele¬conferences, and other activities. Patient advocates have been actively involved in all areas of caBIGā„¢ from the beginning, to ensure that the needs of patients are addressed.

Industry and Other Partners

  • NCI welcomes the involvement of commercial and other groups as part of caBIGā„¢. Currently, several commercial organizations and nonprofit organizations participate in caBIGā„¢ activities. These organi¬zations include information technology companies, large-scale software vendors, pharmaceutical companies, and biotechnology companies, as well as small, specialized ventures. Participation varies from occasional involvement in open meetings to regular involvement with specific caBIGā„¢ Workspace activities. Some vendors are modifying their products to be caBIGā„¢ compatible. Others are competing for software development contracts. Key standards development organizations such as Health Level 7 (HL7) and Clinical Data Interchange Standards Consortium (CDISC) are also engaged.

What is the incentive to become a caBIGā„¢ adopter?
caBIGā„¢ adopters help identify the requirements for caBIGā„¢ tools. They gain early access to the tools; and they install, implement and report on the tools to improve them. Issues such as compatibility of legacy applications as well as future application designs are important areas of focus in the development of an interoperable caBIGā„¢ system. Partner participation provides valuable input in both the assessment of need as well as the definitions of the solutions.


How does caBIGā„¢ work?

How are the activities of caBIGā„¢ structured and managed?
caBIGā„¢ is a consortium of cancer researchers, informaticists, and other partners in the public and private sectors who work collaboratively to develop, adopt and implement interoperable infrastructure and tools. caBIGā„¢ activities are organized into workspaces (nine currently), which are the primary sources of program priorities and substantive work. Together, these groups lead the activities of caBIGā„¢ and build its foundation. The initiative overall is actively managed by a general contractor and the National Cancer Institute.

What are the key elements of caBIGā„¢?
Following are the key elements of caBIGā„¢

Bioinformatics and Biomedical Informatics

  • The field of bioinformatics, broadly defined as the application of information technology and its tools in biologic disciplines, includes sophisticated computing capabilities and analytical methodologies to manage the large volumes of data generated in molecular biology and genomics. Biomedical informatics provides infrastructure and tools to bridge research and health care, pointing toward the delivery of patient-centric molecular medicine.

Community

  • The caBIGā„¢ program helps to build the community of physicians, researchers, information technology professionals and patients that is essential for the creation and delivery of improved cancer treatments. This community provides the sociological infrastructure for interoperable data systems, data sharing and data standards.

Standards for Semantic Interoperability

  • The caBIGā„¢ compatibility guidelines provide a framework for true semantic interoperability, that is, the ability for one system to obtain and use information that resides in another system. These guidelines are designed to operate in a federated environment, allowing individuals to express their scientific creativity while still building systems that can interact with each other. In addition, caBIGā„¢ has an active data standards activity, utilizing a consensus based approach for standardizing the representation of certain types of data.

Grid Computing

  • Grids are groups of computers that use networks and standard communications protocols to integrate their functions, share data, and share processing resources. The computers that make up a grid may be widely distributed within a region or even around the world. Grids that focus on sharing data are referred to as ā€œdata grids,ā€ while those that focus on sharing computer processing capacity are called ā€œcompute grids.ā€ caBIGā„¢ is a data grid using open Web Services communications standards. caBIGā„¢ is building grid software based on Open Grid Services Architecture (OGSA and OGSA-Data Access Integration [OGSA-DAI]) and the Globus Toolkit from Globus Alliance (http://www.globus.org/ogsa/), a leading open-source grid computing project. Work within caBIGā„¢ applies the OGSA standards to biomedical research needs. They are the basis for the development of a prototype system that satisfied simple data integration and sharing use cases. As is typical for open-source projects, the caBIGā„¢ work extends these standards in application-specific ways and contributes new ideas back to Globus Alliance for possible inclusion in the overall grid standards. The advantage of true grid architecture such as OGSA is that each computer runs standard grid software that enables the computer to do the following:
    • Participate in the grid
    • Locate resources in the grid for local use by programs or users
    • Contribute resources to the grid for remote use
    • Provide for data security and other necessities
    Software developers and researchers designing tools for data analysis and user interaction can focus on research requirements with the knowledge that the grid will handle the previously mentioned jobs appropriately.

Where can I find information on the grid infrastructure for the caBIGā„¢ initiative?
General information about the grid infrastructure is presented in a white paper, available at https://caBIG.nci.nih.gov/guidelines_documentation/caGRIDWhitepaper.pdf. caGrid version 0.5 was released in 2005, and is available at https://caBIG.nci.nih.gov/workspaces/Architecture/caGrid. Version 1.0 will be available in the Fall of 2006. Additional information of caGrid, including scenarios and use cases, can be found at https://caBIG.nci.nih.gov/workspaces/Architecture.

What is meant by ā€˜caBIGā„¢ compatibility’?
The caBIGā„¢ program is meant to be federated, that is, development is carried out locally by participating groups using their best scientific judgment, rather than being directed centrally. In order to make such systems interoperable, caBIGā„¢ focuses on the interfaces to software systems and on the way in which systems are described. To aid in the creation of software that will be able to interoperate within the caBIGā„¢ program, a set of compatibility guidelines (https://caBIG.nci.nih.gov/guidelines_documentation) was developed that spells out requirements for interoperability in areas of Interface Integration, Vocabularies/Terminologies and Ontologies, Information Models and Data Elements. Systems that meet the requirements are said to be ā€œcaBIGā„¢ Compatible.ā€ Interoperability is not all or nothing, but rather there exists a range of interoperability; hence the guidelines provide requirements for different ā€˜Maturity Levels’ from Legacy (closed) to Gold (fully open). Thus a system is judged to be compatible at a particular maturity level.

What are the current caBIGā„¢ compatibility levels?
The caBIGā„¢ community recognizes that there can be differing degrees of interoperability between systems, and that these can be quantified in terms of maturity level. The caBIGā„¢ Compatibility Guidelines are thus organized into four levels of maturity: Legacy, Bronze, Silver, and Gold, as defined below. Each maturity level reflects an increasing degree of interoperability with other caBIGā„¢ applications.

Legacy

  • Legacy compliance implies that interoperability with an external system or resource is unlikely. This category is included for systems that were designed either before or without an awareness of the caBIGā„¢ Compatibility Guidelines. Systems identified as legacy-compliant do not meet the requirements for interoperability with caBIGā„¢.

Bronze

  • The bronze compliance level requires that a minimum set of requirements must be met. These requirements ensure a minimal degree of interoperability with caBIGā„¢.

Silver

  • The silver compliance level requires that a rigorous set of requirements be met. These requirements significantly reduce the barriers to use of a caBIGā„¢ resource by a remote system that was not involved in the development of that resource.

Gold

  • The gold compliance level is currently being defined by the caBIGā„¢ community. When defined, the gold compliance level will delineate a formalized grid architecture and data standards that will enable standardized advertising, discovery, and use of all federated caBIGā„¢ resources.

How is caBIGā„¢ Compatibility Evaluated?
For software developed or adopted under the auspices of the caBIGā„¢ program, the determination of caBIGā„¢ compatibility is made by a formal review conducted by the cross-cutting workspaces. At this time, only ā€˜Silver’ compatibility reviews are being conducted for caBIGā„¢ developed systems; the ā€˜Gold’ level review process will be developed after the finalization of the caGrid 1.0 Architecture. For software built outside of the auspices of the caBIGā„¢ program, the NCICB has established the first phase of a caBIGā„¢ compatibility review pro¬cess. This initial process, for Bronze compatibility, is a verified self-test, and is outlined on the caBIGā„¢ Web site at https://caBIG.nci.nih.gov/guidelines_documentation. Vendors whose products have completed this process will receive a license to call the product ā€œcaBIGā„¢- Bronze compatible.ā€ NCICB and the caBIGā„¢ cross-cutting workspaces are also exploring the creation of a formal process for certifying the Silver- or Gold-level compatibility of applications developed outside of the caBIGā„¢ program. Although there is currently no mechanism to certify compliance beyond Bronze, adherence to the existing compatibility guidelines will facilitate certification in the future.

What is the status of caBIGā„¢ compatibility certification for commercial systems?
The caBIGā„¢ Bronze Compatibility Certification Process has now been established (see above). The NCI and caBIGā„¢ will use the experience of the Bronze program, as well as the ongoing ā€˜Silver’ interoperability reviews performed by the cross-cutting workspaces and input from the caBIGā„¢ community (including our industry partners) to develop the formal ā€˜Silver’ and/or ā€˜Gold’ certification process.

What can be said about an application that is intended to be caBIGā„¢ compatible and has been developed in compliance with the compatibility guidelines, but has not been certified?
Such an application or organization could be described as ā€œplanned to be caBIGā„¢ compatible;ā€ ā€œseeking certification;ā€ or even ā€œintended to be consistent with caBIGā„¢ compatibility guidelines as they emerge.ā€ An application that has not been certified cannot be described as ā€œcaBIGā„¢ compatibleā€ without violating the caBIGā„¢ trademark.

Can a commercial application that was not created as a caBIGā„¢ application be converted into a caBIGā„¢-compatible application? If so, does the resulting application become open source?
A commercial vendor can create or retro-fit an application and make the application caBIGā„¢-compatible. This can be achieved by following the caBIGā„¢ Guidelines and successfully completing the formal verification process for certifying caBIGā„¢ compatibility, when that process becomes available. Since this process is not funded as part of caBIGā„¢, the resulting application and its code are not required to be open source.

Does any development work done by a commercial organization for a cancer center on caBIGā„¢ - funded work or directly funded through a competitive Request For Proposals (RFP) and contract become open source?
Yes, the development done by a commercial vendor for the participating cancer center or directly funded through a competitive RFP and contract becomes open source since this development is funded by the caBIGā„¢ initiative. All funded caBIGā„¢ projects must comply with the caBIGā„¢ principles – open source, open access, open development and federated. The cancer center is funded to either create or retrofit applications to be caBIGā„¢ compatible, so this development by the subcontracted vendor becomes open source.

How will caBIGā„¢ ensure that data shared across centers will be secure and that the privacy of human subjects will be upheld?
Security and privacy-related issues were at the core of the caBIGā„¢ planning process. caBIGā„¢ has formed the Data Sharing and Intellectual Capital Strategic Level Workspace to address these issues as part of its charter. The Architecture Workspace is addressing the technical aspects of these important issues. A White Paper detailing security practices is available at https://caBIG.nci.nih.gov/workspaces/Architecture/caBIG_Security_Technology_Evaluation_White_Paper_20060123.pdf.

Can anyone download a caBIGā„¢ application?
Anyone can download any desired software from the caBIGā„¢ Web site. Tools are listed on the Inventory of Tools page at https://caBIG.nci.nih.gov/inventory. caBIGā„¢ applications are released under a non-viral open source license; and can be incorporated into derivative works by both commercial and non-commercial entities.

How is caBIGā„¢ funded?
caBIGā„¢ is funded through contracts, not grants, with specific deliverables and milestones. Contracts may be issued directly by NCI or through subcontracts issued by the General Contractor. Funds support the caBIGā„¢ activities of the cancer centers participating in the pilot phase of caBIGā„¢ and competitive contracts for software development and other activities.


Industry Partners FAQs

What are the benefits to commercial organizations of participating in caBIGā„¢?
Vendors will find growing demand for their products. As they make their products caBIGā„¢ compatible, their systems and applications will meet the needs of a growing number of cancer centers, which will increasingly require caBIGā„¢ compatibility as part of the software acquisition process. Systems that are caBIGā„¢-compatible are able to access both caBIGā„¢-related data sources and grid-available tools, providing new opportunities, features, and methodologies. ā€Realā€ research data for testing and demonstration of commercial organization’s systems will be more easily accessed via the caBIGā„¢ network. Information for commercial organizations are listed on the caBIGā„¢ Web site (https://caBIG.nci.nih.gov/for_vendors). Direct funding may be available for commercial organizations from caBIGā„¢ through openly competed RFPs, posted on the caBIGā„¢ Web site as they become available. Companies can also choose to work with a cancer center on caBIGā„¢ - funded projects, as long as the caBIGā„¢ guidelines are followed.

Can a commercial organization take the open source software that they have developed with caBIGā„¢ funding (directly, or indirectly from a Cancer Center) and use this in existing applications? Can applications with this incorporated code be marketed and sold?
Yes. Commercial organizations can take a freely available open source piece of software and incorporate it into existing code base. Such applications can be marketed and sold by the commercial organization.

How can commercial organizations share caBIGā„¢ compatible applications with the caBIGā„¢ community?
The caBIGā„¢ Web site will include software solutions which are caBIGā„¢-compatible and of interest to the community. NCI hopes that there will eventually be a rich variety of tools and services from throughout the vendor community that interoperate with the caBIGā„¢ network.

How can commercial organizations participate in the caBIGā„¢ initiative?
There are a variety of ways commercial organizations can participate on a voluntary basis in caBIGā„¢ activities:

  • Track activities on the caBIGā„¢ Web site at https://caBIG.nci.nih.gov.
  • Sign up for the ā€œannounceā€ list ser- vice for caBIGā„¢ to receive regular updates on caBIGā„¢ activities and events. This list service is open to all interested parties and can be found at
    https://list.nih.gov/archives/cabig_announce.html.
  • Attend open caBIGā„¢ Workspace meetings (teleconferences as well as periodic face-to-face gatherings). These are listed in ā€œWhat’s BIG this Weekā€ (https://caBIG.nci.nih.gov/News_Folder/WBTW) a weekly update sent to everyone on the ā€œcaBIGā„¢_announceā€ list service. In addition there is a Calendar of events on the caBIGā„¢ Web site, updated weekly, available at https://caBIG.nci.nih.gov/events/. (Note: If meeting space is limited, precedence is given to funded caBIGā„¢ participants.)
  • Attend the caBIGā„¢ 2007 Annual Meeting. Information will be posted at https://caBIG.nci.nih.gov/ events/events_webcasts_town halls and on the home page as the event approaches.
  • Work toward making a company’s applications and solutions caBIGā„¢ - compatible. Guidelines for caBIGā„¢ compatibility are available at https://caBIG.nci.nih.gov/ guidelines_documentation. Certification processes for caBIGā„¢ compatibility are being developed and will be announced on the Web site.
  • Integrate into a company’s systems the available open-source software, tools, and standards developed by the funded caBIGā„¢ project activities. An inventory of caBIGā„¢ tools, data, and standards, as well as the associated NCICB infrastructure, are available at https://caBIG.nci.nih.gov/inventory/.
  • Contribute technologies, tools, or components that are relevant and compatible with caBIGā„¢ and that are not intended to be commercialized under a proprietary licensing arrangement.
  • Watch the archived caBIGā„¢ webcasts about specific areas of technical interest. These webcasts can be accessed on the caBIGā„¢ Web site at https://caBIG.nci. nih.gov/webcasts/. NCI hosted its first caBIGā„¢ Industry Partners Meeting on September 30, 2005. Industry representatives learned about the caBIGā„¢ compatibility requirements and commercial opportunities in the caBIGā„¢ program. Information on the meeting can be found at https://cabig.nci.nih.gov/2005_Industry_Partners/.

Are there opportunities for commercial organizations to assist NCI with the coordination and support of the caBIGā„¢ initiative?
Currently, several commercial organizations contract with the NCI to assist with some of the coordination and support activities for caBIGā„¢. Any future related opportunities in this area will be solicited via the usual Federal Government Procurement mechanisms.


More Information and getting Involved

How can I learn more about caBIGā„¢?
The caBIGā„¢ Web site (https://caBIG.nci.nih.gov) is updated continually with related activity information. Specific resources also include:

How do I get involved with caBIGā„¢?
There are many ways that you can become involved with caBIGā„¢:

  • Track caBIGā„¢ activities and progress on the National Cancer Institute’s caBIGā„¢ Web site at https://caBIG.nci.nih.gov.
  • Attend open caBIGā„¢ meetings to contribute ideas and to better understand caBIGā„¢ activities. Watch the caBIGā„¢ Web site for information on these types of opportunities via the calendar on the right side of the Web site, or the Events folder located in the left navigation bar.
  • Attend the caBIGā„¢ 2007 Annual Meeting. Information will be posted at
    https://caBIG.nci.nih.gov/events/events_webcasts_townhalls and on the home page as the event approaches.
  • Learn more about the NCI’s existing bioinformatics infrastructure - caCORE - as caBIGā„¢ is harnessing the strengths of this platform and activities will be undertaken in a complementary way.
    Further information is available at the NCICB Web site via the following link: http://ncicb.nci.nih.gov/NCICB/ infrastructure.
  • Download and become familiar with the tools and applications already available on the caBIGā„¢ Web site. This is only the beginning, and this list will start to grow rapidly over the next few months as more informatics
    applications become interoperable and available to share. The current inventory of infrastructure, applications, and datasets used to support the caBIGā„¢ initiative can be accessed at the caBIGā„¢ Web site. This inventory includes key infrastructure and applications from the National Cancer Institute Center for Bioinformatics and can be found via the Inventory of Tools section at https://caBIG.nci.nih.gov/inventory.
  • Start to think about how you could integrate the tools and databases you are developing into the caBIGā„¢ community.
  • Sign up for the caBIGā„¢ mailing list at https://list.nih.gov/archives/caBIG_announce.html to receive important notices about current and upcoming activities.

As the caBIGā„¢ community continues to grow, additional infrastructure, tools and data will be made available. Furthermore, resources and informational tools will be provided by the caBIGā„¢ community and the NCI to assist those who want to use or contribute to the network. These will include training resources, support for use and adoption of tools, informational Workshops, and tools to facilitate broader use of caBIGā„¢ by interested organizations.

 

Reference:
cabig.nci.nih.gov (2006). About caBIG.Ā  Retrieved September 15, 2008, from https://cabig.nci.nih.gov/overview?pid=primary.2006-07-07.4911641845&sid=about&status=True

cabig.nci.nih.gov (2006). caBIG FAQs.Ā  Retrieved September 15, 2008, from https://cabig.nci.nih.gov/faqs