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National Cancer Informatics Program (@NCIP)

NCIP

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gdc-docs

Official repository for GDC User Guides in Markdown format

annotation-and-image-markup

Annotation and Image Markup (AIM) is the first project to propose and create a standard means of adding information and knowledge to an image in a clinical environment, so that image content can be easily and automatically searched.

national-biomedical-image-archive

The National Biomedical Imaging Archive (NBIA) is a free and open source service and software application that enables users to securely store, search, and download diagnostic medical images, providing a searchable national repository integrating in vivo cancer images with clinical and genomic data. Using role-based security, NBIA provides web-based access to de-identified DICOM images, image markup, annotations, and rich meta data.

pathway-interaction-database

The Pathway Interaction Database (PID) is software supporting the access and display of information about bio-molecular interactions and cellular processes assembled into signaling pathways.

lexevs

The LexEVS Terminology Service.

alview

Alview : Alignment View for BAM files - a fast,portable tool for viewing short reads as native GUI program, command line or via webserver

catissue-core

caTissue Suite is a modular, open-source, specimen inventory and tracking system.

lexevs-service

A CTS2 Framework Service Plugin based on LexEVS

caadapter

caAdapter provides model mapping, data mapping and transformation services among data sources like HL7 and Regulatory Data Sets.

nci-metathesaurus-browser

The NCI Metathesaurus (NCIm) Browser is a web-based terminology browser that allows users to browse and search the NCI Metathesaurus, a biomedical terminology database that maps terms from more than 70 terminology sources into some 1.5 million biomedical concepts.

xmihandler

The XMI Handler provides a set of APIs to read from and write into XMI files. The XMI Handler parses a given XMI file and represent the model in Java objects. The APIs work with both ArgoUML and Enterprise Architect created XMI models.

labviewer

LabViewer is a web application used to view and store clinical laboratory data

caaers

caAERS is a web application for recording and reporting adverse events that occur during cancer clinical trials

cacore-sdk

The caCORE Software Development Kit (SDK) generates a system built on the principles of Model Driven Architecture (MDA), n-tier architecture and a common API for data access. 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."

cagrid-core

The caGrid core infrastructure project includes the caGrid core services and tooling, which enables the National Cancer Informatics Platform's interoperability strategy.

cananolab

caNanoLab is a web-based portal designed to capture nanotechnology data.

psc

Patient Study Calendar is a web application for tracking patients in clinical trials.

cgr-bambino

Bambino: SNP caller and Alignment Viewer for Next Gen Data

nci-diff-CDISC

diff specific for CDISC reports

Trinity_CTAT_galaxy

Files needed for Galaxy tools used to run Trinity_CTAT workflows.

ctat-metagenomics

common-security-module

The Common Security Module (CSM) provides a comprehensive solution to common security objectives, with flexible delivery of security tools to allow application developers to integrate security with minimal coding effort. This helps eliminate the need for development teams to create their own security methodology. CSM provides solutions for authentication, authorization, and user provisioning.

nci-term-browser

The NCI Term Browser is a web-based browser that allows users to search all terminologies, value sets and mappings on the LexEVS terminology server, to browse individual sources, and to easily follow the many links that connect them.

nci-mapping-tool

The NCI EVS Mapping Tool supports mapping between term lists, value sets, terminology subsets, or whole terminologies using a mix of automated and manual methods. This initial prototype release is used internally by EVS, but will need further development to reach a broader user community.

cagrid2

The caGrid2 project includes enhancements to the caGrid core services to support WS* and SHA2, which enables the National Cancer Informatics Platform's interoperability strategy.

c3pr

C3PR is a web-based application that can be used for end-to-end registration of patients in clinical trials.

cabio

caBIO (cancer Bioinformatics Infrastructure Objects) is a resource for accessing molecular annotations from curated data sources.

caaers-docs

This is the documentation repository for Cancer Adverse Event Reporting System (caAERS) project that is under the NCIP channel

CDR

tcga-sandbox-v1

caarray

caArray is a web-based application supporting the storage, annotation, and sharing of microarray data.

nci-ocr

common-biorepository-model

Common Biorepository Model (CBM) aims to reduce the time and effort required by researchers to locate a biobank that has the specimens they need.

caintegrator

caIntegrator brings together clinical, microarray and medical imaging data for integrative data query and analysis.

ncip.github.com

This is the repository for the NCIP channel page. It hosts the wiki pages and the issue tracker related to the migration activity.

cadsr-cde-browser

The CDE Browser is the primary starting point for exploring the contents of the caDSR.

cagrid-docs

The caGrid-docs repository contains caGrid-related documentation, including Admin/Developer/User guides, design documents, and presentations.

edct-formbuilder

Enterprise Data Collection Tool (eDCT) Form Builder allows users to design data collection instruments utilizing a “drag-and-drop” interface.

invivo-imaging-middleware

The In Vivo Imaging Middleware (IVIM) (better known as IVI Middleware) is a set of open source tools and middleware that provide interoperability between DICOM and the caGrid. IVIM development is driven by common use cases from radiology and pathology for common activities, such as central review in image-based clinical trials and data and application sharing in secure high-performance environments.

common-logging-module

Common Logging Module (CLM) is a set of tools that provides a flexible and comprehensive solution for auditing and logging. CLM includes Event Logging, Automated Object State Logging, Asynchronous Logging to database, Query API's and a web based Log Locator Tool.

cadsr-cdecurate

The CDE Curation Tool supports creation and editing of Data Element Concepts, Value Domains, and Data Elements.

nci-value-set-editor

The NCI EVS Value Set Editor is used to create and maintain CTS 2 value set and pick list definitions for loading into the LexEVS terminology server, which resolves the definitions against referenced terminologies. This initial prototype release is used internally to generate all value sets published by EVS, but will need further development to reach a broader user community.

CDR-Lite

Generic version of the CDR, updated to remove study-specific references

iso21090

ISO 21090 Localization Common Library is a specializead and constrained version of the ISO 21090 Healthcre Data Types. Localization is the list of approved ISO 21090 data types created by CBIIT, along with common implementation artifacts.

ctms-commons

A collection of libraries for shared functionality across the CTMS workspace, and particularly among the applications in the Clinical Trials Suite.

catissue-print-service

The caTissue Print Service provides the framework for printing labels for specimens, specimen collection groups and containers from the caTissue application.

c3pr-docs

This is the document repository of the c3pr project under the NCIP channel.

cagrid-grid-incubation

caGrid-grid-incubation contains projects that use or enhance caGrid, that were contributed by the community.

lexevs-remote

A remote (RMI) access wrapper around LexEVS.

tcga-sandbox

lexevs-grid

caGrid Analytical and Data services for LexEVS.

camod-docs

This repository holds documents for the Cancer Models Database(caMOD) project under the NCIP channel.

qfive

QFive provides a probabilistic classification algorithm using the spectra from either SELDI or MALDI-TOF mass spectrometry results as input.

camod

The cancer models database (caMOD) provides information about animal models for human cancer to the public research community.

wustl-common-utilities

WUSTL Common Utilities is a Open Source project primarily used by caTissue Suite.

ihub

iHub enables data integration between a clinical data management system (CDMS) and clinical trial management applications such as caTissue and the Cancer Adverse Event Reporting System (caAERS).

URI_Resolver

Resolves URIs for CTS2

cacis-docs

This repository contains all the documentation for the Clinical Information Suite (caCIS) project under the NCIP channel.

rembrandt

REMBRANDT (REepository of Molecular BRAin Neoplasia DaTa) database was developed to allow analysis of data from molecularly characterized primary brain tumors and correlate those data with extensive retrospective and prospective clinical data.

clinical-connector

Clinical Connector enables the integration of participant registration and laboratory data between the Cancer Central Clinical Database (C3D) and the C3PR and LabViewer clinical trial management applications.

cacore-sdk-docs

This repository holds documents for the caCORE SDK project under the NCIP channel. See https://github.com/NCIP/cacore-sdk for further information.

caobr

caOBR (Cancer Open Biomedical Resources) is a tool for indexing cancer informatics resources within the NCBO (National Center for Biomedical Ontologies) Resource Index.

edct-collector

The eDCT Collector is designed to collect and store data submitted to the system in accordance with the model designed in eDCT Form Builder.

cacore-sdk-pre411

This is caCORE SDK pre 4.1.1 version repository. These releases are not being supported. Please visit cacore-sdk repository for current development.

cadsr-semantic-tools

The Semantic Integration Workbench (SIW) is a caCORE tool that assists users in adding consistent metadata to a UML model, or verifying consistency, by tagging their domain model with matching concepts from the NCI Thesaurus.

catissue-migration-tool

The Migration Tool is a java application, based on the API and developed within the caTissue project. The migration involves extracting input legacy data into an interim caTissue staging database and then running the caTissue Migration Tool, which will validate and load the staging data into the target caTissue instance.

calims

caLIMS is a Laboratory Information Management System (LIMS) that tracks a complete laboratory workflow to generate experimental results for data repositories or data management services.

cab2b

cancer Bench-to-Beside (caB2B) is an open-source query tool that permits translational research scientists to search and combine data from virtually any caGrid data service.

cacis

The Cancer Clinical Information Suite (caCIS) project contains the middleware components that allow source system to transmit the clinical data to the recipient systems using different transmission formats as well as protocols.