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This page
provides easy access all available NCICB
software components and tools. Items are sorted
alphabetically. Use the links below to jump to a
particular section.
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C3PR (Cancer Central Clinical Participant Registry)
NCI’s Cancer Central Clinical Participant Registry (C3PR) is a cornerstone application in the caBIG Clinical Trial Management System (CTMS) portfolio. The application registers patients to clinical trials and provides interoperability with other CTMS applications via both Web Services and cancer Common Ontologic Representation Environment (caCORE) Software Development Kit (SDK) Generated APIs. In addition, integration via Web Services with the Cancer Central Clinical Database (C3D) makes the C3PR Application a time saver for C3D adopters.
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caAdapter is an open source tool set that provides model mapping services in support of caCORE components and facilitates data mapping and transformation among different kinds of data sources including HL7 v2 messages, HL7 v3 messages, and Regulatory Data Sets. caAdapter has a component-based architecture to support message development and reporting using standard data formats. It also integrates with other clinical trials applications such as caXchange. caAdapter provides web service access and APIs for easy application integration.
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caArray is data management system guiding the annotation and exchange of array data through a federated model of installations. It provides browser-based and programmatic access to the data stored locally; enables mechanisms for accessing all local installation data over caGrid; supports compatibility with caBIG guidelines, and promotes compatibility with the MIAME 1.1 guidelines.
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The cancer Bioinformatics Infrastructure Objects (caBIO) model and
architecture was the first model-driven information system built using cancer Common Ontologic Representation Environment (caCORE), and formed the basis for caCORE architecture. Each of the caBIO domain objects represents an entity found in biomedical research such as Gene, Chromosome, Sequence, SNP, Library, Clone, and Pathway. Examining the relationships between these objects can reveal biomedical knowledge that was previously buried in the various primary data sources. caBIO data can be accessed via a robust, platform-independent set of data services developed using the caCORE data integration techniques. Researchers are able to perform innovative analysis on caBIO data via a variety of APIs,
web services and html interfaces. This download provides access to the caBIO source code, web services, java client.jar files, programming interfaces, documentation and more.
The caBIO 4.x+ release involved a separation of caBIO from the caCORE infrastructure to allow for continued and frequent enhancements to caBIO genomic annotations. As such, caBIO 4.x provides support for the caBIO API only. Access to the caCORE 3.2 release, which contains caBIO, the caDSR, and EVS APIs is available for download on the caBIO download site in the archives section of the page. The caBIO 4.x licensing agreement applies.
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NCICBIIT provides biomedical informatics support and integration capabilities to the cancer research community. NCICBIIT has created caCORE Software Development Kit (caCORE SDK), a data management framework designed for researchers who need to be able to navigate through a large number of data sources. The caCORE SDK generated system is built on the principles of Model Driven Architecture (MDA), n-tier architecture & common API for data access. The use of MDA and n-tier architecture allows for easy access to data, particularly by other applications.
When the caCORE SDK generated system is combined with controlled vocabularies and registered metadata, the resulting software system, called “caCORE-like” system is “semantically integrated” – all exposed API elements have runtime accessible metadata that defines the meaning of the elements using controlled terminology
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| caDSR (Cancer Data Standards Registry and Repository) |
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The Cancer Data Standards Registry and Repository (caDSR) is database and a set of APIs and tools based on the ISO/IEC 11179 Information Technology Metadata Registries (MDR) standard.
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The cancer Biomedical
Informatics Grid, or caBIG, is a voluntary
network or grid connecting individuals and
institutions to enable the sharing of data and
tools, creating a World Wide Web of cancer
research. The goal is to speed the delivery of
innovative approaches for the prevention and
treatment of cancer. The infrastructure and
tools created by caBIG also have broad utility
outside the cancer community. The approach is to
leverage existing technologies for the
standardization of data representation and
semantics coupled with a common data integration
architecture. This data grid will help to expose
existing and new data sets as grid data
resources. caGrid is expected to enable the
building of an open, multi-institutional data
sharing, annotation, and analysis environment.
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Cancer Genome-Wide Association Studies (caGWAS) allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. New breakthroughs in SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations.
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caIntegrator is a translational application framework that allows researchers and bioinformaticians to access and analyze clinical and experimental data across multiple clinical studies. This application framework provides a mechanism for integrating and aggregating biomedical research data and provides access to a variety of data types (e.g. microarray-based gene expression, Immunohistochemistry, SNPs, clinical trials data etc.) in a cohesive fashion. This knowledge framework offers a paradigm for rapid sharing of information and accelerates the process of analyzing results from various biomedical studies with the ultimate goal to rapidly change routine patient care.
caIntegrator provides a framework with the necessary infrastructural components needed to develop enterprise level translational applications. This caIntegrator application framework comprises an n-tier service oriented architecture that allows pluggable web-based graphical user interfaces, a business object layer, server components that process the queries and result sets, a data access layer and a robust data warehouse. Service APIs are provided that enable the application clients to be agnostic of the details of how the biomarker findings are created.
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caLIMS is an “open source” web based Laboratory Information Management System (LIMS) designed to automate workflow in the laboratory. caLIMS operations include user and laboratory administration, inventory management, project creation, project execution, and experimental results capture. The LIMS is extensible to accommodate the needs of laboratories performing diverse assays using varying technologies. caLIMS has been updated with the release of lpgLIMS 1.3 (see lpgLIMS 1.3).
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| caMassClass |
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caMassClass is a package of R
functions for reading, processing and
classification of protein mass spectra (SELDI)
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| caNanoLab |
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The cancer Nanotechnology Laboratory (caNanoLab) is a data sharing portal designed to facilitate information sharing in the biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab allows researchers to share information on nanoparticles including the composition of the particle, the functions (e.g. therapeutic, targeting, diagnostic imaging) of the particle, the characterizations of the particle from physical (e.g. size, molecular weight) and in vitro (e.g. cytotoxicity, immunotoxicity) nanoparticle assays, and the protocols of these characterization.
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| caBIG® Clinical Trials Suite |
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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. Version 1.1 of the Suite includes the following applications: C3PR v2.5, caAERS v1.5, PSC v2.3, CTODS Lab Viewer v1.5, caXchange v1.5, and C3D Connector v1.2. The caBIG® Clinical Trials Suite is designed to support a range of key tasks, such as screening and registering patients for accrual on clinical trials; scheduling and tracking of patient activities during the course of a study; integrating laboratory results with the patient record; tracking, managing and reporting adverse events; and capturing, storing, analyzing and routing clinical data in a meaningful manner. The bundle also contains software tools that facilitate electronic connection of local clinical data management system investments to the caBIG® network. The Suite also provides security features and access controls to ensure appropriate protection of human subject information and clinical research data.
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CGEMS-CGOM APIs demonstrate various ways to execute searches from any CGEMS object within the Clinical Genomic Object Model (CGOM) using caIntegrators's Object Query Service, they provide programmatic access to the following datasets from the NCI CGEMS study:
- SNP Association Findings
- Population Frequency
- SNP Assay and Panel information
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| Common Logging Module (CLM) |
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The NCICB Common Logging Module (CLM) was chartered to provide a comprehensive solution to Audit and Logging objectives and also to prevent the duplication of the effort and time involved in developing a logging solution. CLM is flexible enough to allow application developers to integrate audit logging into almost any code design with minimal coding effort. This phase of the Common Logging Module brings the NCICB team one step closer to the goal of CFR 21 / part 11 (FDA) compliance. The CLM features include Event Logging, Object State Logging, Asynchronous Logging to database, Query API's and a web based Log Locator Tool.
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| CSM (Common Security Module) |
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The NCICB Common Security Module (CSM) provides a flexible solution for application security and access control. CSM is intended to be used as a common starting point for any development team that has security requirements, and thus helps to avoid duplication of effort and inconsistent security implementations. CSM has three main functions: Authentication to validate and verify a user's credentials; Authorization to grant or deny access to data, methods, and objects; and User Authorization Provisioning to allow an administrator to create and assign authorization roles and privileges.
CSM offers an additional solution that works with the caCORE Software Development Kit (SDK). CSM-SDK Adapter, provides the ability to integrate CSM security, session management, and writeable APIs into SDK generated software.
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| EVS (Enterprise Vocabulary Services) |
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The NCI Thesaurus and Metathesaurus provide standard vocabularies for cancer research. The content of the NCI Thesaurus is available for download in ASCII flat file format, Ontology Web Language (OWL) format and in Apelon's proprietary Ontylog XML format.
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LexEVS is the primary application programming interface to the EVS terminology server (LexBIG). This download provides access to the LexEVS source code, web services, java client.jar files, programming interfaces, documentation and more. LexEVS APIs provide access to vocabulary data and are based on the 3.2 domain model or LexBIG service model depending on which of the APIs a client application interfaces with. Access to the earlier releases of the EVS APIs is available for download from the EVS Archives page.
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lpgLIMS 1.3 is an "open source" web based Laboratory Information Management System (LIMS) designed to capture research laboratory workflow. lpgLIMS 1.3 functions include user and laboratory administration, inventory management, project creation, project execution, and experimental result storage. lpgLIMS 1.3 is an enhanced version of caLIMS 1.2. It features a variety of bugfixes and streamlined build and installation procedures for rapid deployment on Windows, Linux and Solaris. The lpgLIMS 1.3 distribution includes templates for common genomic assays as well as adapters for data files produced in experiments using Applied Biosystems sequencers and Affymetrix gene expression and genotyping microarrays. lpgLIMS 1.3 can be extended to accommodate the needs of laboratories performing assays using diverse technologies. lpgLIMS 1.3 is not a caBIG compliant application. Domain concepts from lpgLIMS 1.3, caLIMS 1.2 and caLAB will be used as the basis for a new initiative, caLIMS II, which will produce a full featured, caBIG compliant LIMS. Anyone interested in contributing to this effort is invited to join the NCICB LIMS Consortium.
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The tools brought together in the Life Sciences Distribution facilitate the discovery of the next generation of cancer diagnostics and therapeutics to realize the vision of Molecular, or Personalized Medicine. They support a variety of capabilities from tracking and managing biospecimens, to analyzing and integrating microarray data. Together, they enable cancer researchers to more easily integrate, analyze and share data from many different sources.
All caBIG™ Life Sciences Distribution components can be plugged into the national caGrid backbone that connects caBIG™ informatics resources across research organizations.
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The LSD Browser is a free-form search tool intended to provide a simple single search interface allowing users of the caBIG® Life Sciences Distribution tools to query across local, remote, and NCICB instances of these tools. LSDB also provides users a single point of access to their local installations of life sciences research tools. The current version of the LSDB can search across instances of NCIA and caArray. Future releases will provide search access across the other LSD applications.
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The in vivo image repository provides the cancer research community, industry, and academia with access to image archives that can be used for many purposes including the potential to assist in the development and validation of analytical software tools supporting: lesion detection and classification software, accelerated diagnostic imaging decision, and quantitative imaging assessment of drug response. The repository provides access to imaging resources that will improve the use of imaging in today's cancer research and practice by: increasing the efficiency and reproducibility of imaging cancer detection and diagnosis, leveraging imaging to provide an objective assessment of therapeutic response, and ultimately enabling the development of imaging resources that will lead to improved clinical decision support.
- Cedara I-Response Client - To visualize images identified on the NCIA search results page, you must have the Cedara I-Response Workstation (IRW) installed on your system.
- NCIA Distribution - Distribution package and installation documentation for installing the NCIA server and NCIA's MIRC server
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Rembrandt web application is the reference implementation of the caIntegrator framework's specifications and interfaces. Rembrandt's graphical user interface is built using Apache's Struts application framework and runs in most of the currently available J2EE Application servers, though the intended platform is JBoss version 4.0.2. The Rembrandt middle-tier implements and/or extends caIntegrator specification interfaces/objects. It utilizes the analysis server for on the fly high order analysis and WGI for visualization of copy number data.
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WebGenome is a web application for creating various types of graphical plots of microarray-based data, especially aCGH data. The system can be configured to read data from relational database systems or from in-memory data structures from client applications
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