Discover NCIP/common-biorepository-model Open Source project

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.

annotation-and-image-markup

C++

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.

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.

pathway-interaction-database

Perl

lexevs

The LexEVS Terminology Service.

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

alview

catissue-core

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

A CTS2 Framework Service Plugin based on LexEVS

lexevs-service

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

caadapter

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.

nci-metathesaurus-browser

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.

xmihandler

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

labviewer

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

caaers

Groovy

cagrid-core

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

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."

cacore-sdk

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

cananolab

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

psc

Bambino: SNP caller and Alignment Viewer for Next Gen Data

cgr-bambino

diff specific for CDISC reports

nci-diff-CDISC

Files needed for Galaxy tools used to run Trinity_CTAT workflows.

Trinity_CTAT_galaxy

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.

ctat-metagenomics

Python

common-security-module

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-term-browser

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.

nci-mapping-tool

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.

cagrid2

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

c3pr

Groovy

cabio

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

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

caaers-docs

CDR

tcga-sandbox-v1

caarray

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

Mathematica

nci-ocr

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

caintegrator

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

ncip.github.com

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

cadsr-cde-browser

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

cagrid-docs

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

edct-formbuilder

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.

invivo-imaging-middleware

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.

common-logging-module

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

cadsr-cdecurate

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.

nci-value-set-editor

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

CDR-Lite

Groovy

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.

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

ctms-commons

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

catissue-print-service

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

c3pr-docs

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

cagrid-grid-incubation

A remote (RMI) access wrapper around LexEVS.

lexevs-remote

caGrid Analytical and Data services for LexEVS.

tcga-sandbox

HTML

lexevs-grid

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

camod-docs

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

qfive

camod

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

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

wustl-common-utilities

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).

ihub

URI_Resolver

Resolves URIs for CTS2

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

cacis-docs

XSLT

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 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.

clinical-connector

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

cacore-sdk-docs

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

caobr

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

edct-collector

PHP

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.

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.

cadsr-semantic-tools

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.

catissue-migration-tool

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.

calims

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.

cab2b