Community development activities: The activities of the four domain workspaces (Integrative Cancer Research, Clinical Trials Management Systems, in vivo Imaging, and Tissue Banks and Pathology Tools), the two cross-cutting Architecture and Vocabulary/Common Data Elements (VCDE) workspaces and the three strategic workgroups (Strategic Planning, Documentation and Training, and Data Sharing and Intellectual Capital) have continued in the Enterprise phase with broader participation from the cancer research community. These activities are essential to the maintenance of a community that supports data sharing, and provides an important mechanism for ascertaining the information technology and standards needs of the cancer research community. The collaboration with the UK National Cancer Research Institute continued with a formal launch at a joint conference in London, UK. In addition, several initial projects have been launched, including a collaboration between US and UK researchers in the area of imaging informatics. Software Development Activities: The caBIG program has continued the development of caBIG compatible infrastructure and user centered software development tools. Two significant developments were initiated during FY2008 with regard to software development: Clinical Trials Interoperability Framework: This bundle of software systems utilizes existing caBIG compatible applications (C3D, C3PR, caAERS, caXchange, CTODS, PSC and the caGrid framework) to create an interoperable system for managing the conduct of clinical trials. The system is designed to be modular, so that particular pieces of functionality can be replaced by existing systems already present at cancer centers and cooperative groups. The target date for release is the middle of FY2008 Life Sciences Distribution: This bundle of software is designed to provide a pre-packaged suite of tools for the conduct of basic biomedical research. This bundle contains caArray (microarray repository), caTissue (tissue banking tool), NCIA (DICOM image archive), CTODS (clinical trials repository) and caGWAS (Genome Wide Association Study data mart). The bundle is designed to utilize a common set of underlying technology and to be modular enough to deploy any combination of the five components. Expected deployment date is Feb 2008. Clinical Trials Working Group (CTWG) Implementation: During FY2008, the implementation of the four informatics initiatives of the CTWG were begun in earnest. These initiatives are: Development of a database to serve as a central source of data for reporting and information sharing on all NCI-sponsored clinical trials. Data submitted to the database will be available to all properly identified users through a unified, web-based interface or portal. Development and implementation of a plan that will enable all NCI-supported internal and external clinical trials systems to seamlessly share standardized information across the NCI cancer research community in a manner that is fully interoperable with NCIs caBIG. Establishment of a core library of harmonized and standardized Phase II and III Case Report Forms (CRFs), incorporating Common Data Elements (CDEs), through stakeholder consensus (including industry and FDA). A secure repository that is accepted by NCI, NCI-sponsored institutions and industry as a single repository for all required and current credentials for investigators and clinical trial sites to conduct clinical trials. In order to begin implementation, four Special Interest Groups or SIGs were created in caBIG. The first goal is the responsibility of the Reporting/Sharing SIG, the second of the Interoperability SIG, the third of the Study Conduct SIG and the fourth the responsibility of the Planning/Monitoring SIG. A CTMS Steering Committee composed of outside experts was created to advise the prime contractor on activities related to the CTWG implementation. The Reporting/Sharing SIG has begun to collect requirements for the clinical trials data base (CTDB) and the Study Conduct SIG has begun work on the first CRF module. Data Sharing and Intellectual Capital: The DSIC workspace has continued its efforts to create a set of data sharing tools (in this case model agreements, policy documents, etc.) to enable secure data sharing of data of a variety of degrees of sensitivity. The major new activity was the initiation of a bundle that will be released with the Life Sciences Distribution and Clinical Trials Interoperability Framework. This bundle, the Data Sharing and Security Framework (DSSF) will be packaged with other caBIG offerings to provide the legal and policy framework to enable data sharing and interoperability on a large scale. Security: The caBIG Enterprise program has created a joint working group (between the DSIC and Architecture Workspaces) to deal with questions of security policy. This group has adopted a set of interim security policies and is currently engaged in creating the policies that caGrid will use during the Enterprise phase. Enterprise Support Network: The caBIG program has launched the Enterprise Support Network (ESN) that will provide a scalable support solution for caBIG as it transitions to the wider network. Ultimately, the ESN will comprise a set of NCI funded Knowledge Centers and Program Offices as well as NCI recognized (but not funded) support service providers. The initial activity of this network was the creation of the caBIG Bronze Compatibility Process that allowed non-caBIG developed software to be certified as Bronze Compatible
| Edmonson, Michael N; Zhang, Jinghui; Yan, Chunhua et al. (2011) Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics 27:865-6 |
| Hesse, Bradford W; Croyle, Robert T; Buetow, Kenneth H (2011) Cyberinfrastructure and the biomedical sciences. Am J Prev Med 40:S97-102 |
| Greenblum, Sharon I; Efroni, Sol; Schaefer, Carl F et al. (2011) The PathOlogist: an automated tool for pathway-centric analysis. BMC Bioinformatics 12:133 |
| Efroni, Sol; Ben-Hamo, Rotem; Edmonson, Michael et al. (2011) Detecting cancer gene networks characterized by recurrent genomic alterations in a population. PLoS One 6:e14437 |
| Zhang, Jinghui; Mullighan, Charles G; Harvey, Richard C et al. (2011) Key pathways are frequently mutated in high-risk childhood acute lymphoblastic leukemia: a report from the Children's Oncology Group. Blood 118:3080-7 |
