National Cancer Informatics Program

Login: NCIP

Company: null

Location: Rockville, MD

email: opensource@nci.nih.gov

Blog: http://ncip.nci.nih.gov/

Members

1. Alex Wilmer
2. Francois G.
3. Juli Klemm
4. Michael Balint
5. Shane Wilson
6. Suhas Khot

Repositories

alview

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

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.

automation

Created as per request NCI-RITM0065579 as part of SVN to GitHub migration

bioconductor

null

bioconductor_v1

null

c3pr

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

c3pr-docs

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

caadapter

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

caaers

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

caaers-docs

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

caarray

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

caarray-docs

This is the documentation repository for caArray project that is under the NCIP channel.

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.

cabio

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

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.

cacis-docs

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

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."

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.

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-admin-tool

The caDSR Administration Tool is the main administrative interface to all of the basic editing and maintenance features and components of caDSR tools.

cadsr-api

The caDSR APIs allow developers to build an application to access caDSR metadata and search the database, or to retrieve caDSR Metadata to customize local data collection applications

cadsr-bulk-loader

The caDSR Bulk Loader uploads metadata from an Excel spreadsheet into the caDSR.

cadsr-cde-browser

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

cadsr-cdecurate

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

cadsr-cgmdr

cgMDR has tools enabling semantic annotation from its own metadata repository but also can resolve metadata and terminologies.

cadsr-cgmdr-nci-uk

cgMDR has tools enabling semantic annotation from its own metadata repository but also can resolve metadata and terminologies.

cadsr-formbuilder

caDSR Form Builder allows users to leverage Common Data Element (CDE) metadata to create forms that replicate the content of Case Report Forms (CRFs).

cadsr-freestyle-search

The caDSR Freestyle Search engine performs weighted semantic searches on the content of Administered Items in the caDSR.

cadsr-grid-dataservice

The caDSR Grid Dataservice is a caGrid enabled dataservice that is generated using caGrid framework.

cadsr-objectcart

The caDSR Object Cart application provides shopping cart-type operations for caDSR data objects.

cadsr-password-change-station

The purpose of the caDSR Password Change Station is to allow users to set and reset the password used for logging in to the caDSR Tools.

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.

cadsr-sentinel

The caDSR Sentinel tool allows users to create and manage Alert Definitions for content in the caDSR

cadsr-uml-model-browser

The caDSR UML Model Browser supports browsing and searching UML Models that have been transformed into caDSR metadata via the UML Loader

cadsr-util

caDSR Utils contains common utility libraries that are used by other caDSR related projects.

caelmir

caELMIR provides the pre-clinical scientist with a data management system to record experimental data.

cagrid

*NOTE* the entire caGrid repository was migrated to capture the total release history, including all branches. Please do not checkout and use this repository, instead use the relevant cagrid-* github project.

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.

cagrid2-wsrf

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.

cagrid-core

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

cagrid-docs

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

cagrid-general

The caGrid-general repository contains third party libraries that are used commonly across the caGrid project.

cagrid-grid-incubation

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

cagrid-iphone-app

iPhone App for caGrid is an application to access services and data on caGrid and a Grid Summary Service to maintain grid information in support of the app.

cagrid-portal

The caGrid-portal repository provides a visualization of caGrid services. It includes the open source Liferay portal container, and several Java JSR-compliant portlets to query and invoke grid services

cagrid-workflow

The caGrid-workflow repository contains the caGrid Workflow Service, which enables orchestration across caGrid services using Taverna's SCUFL language.

cagwas

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

caimage

caImage supports the storage and display of pathology images as well as the capture of and search for annotations associated with those images.

caintegrator

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

caintegrator-data

Data for caIntegrator

caintegrator-docs

This is the documentation repository for the caIntegrator project repository under the NCIP channel.

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.

camod

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

camod-docs

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

cananolab

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

Cancer-Research-Data-Commons-Framework-Documentation

Repository of documentation and technical artifacts related to the NCI CRDC

caobr

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

catissue-advanced-query

The caTissue Advanced Query allows users to query any data in caTissue including complex conditions and associations.

catissue-cacore-sdk

The caTissue caCORE SDK is used by caTissue project to dynamically generate code from a UML model.

catissue-CAS

caTissue Suite uses JASIG CAS (Common Authentication Service) to provide Single Sign-On support with other applications. The caTissue application uses the HTTP request filter provided by CAS to intercept all requests and redirect the user to the Login page in case the user is not already logged in.

catissue-core

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

catissue-dao

null

catissue-docs

The caTissue Docs repository holds the documentation related to the caTissue Core and other caTissue related projects.

catissue-dynamic-extensions

The caTissue Dynamic Extensions allows to quickly make new data or capabilities available in caTissue for discovery and use by the community.

catissue-idp-authentication-manager

caTissue IDP Authentication Manager is an Open Source project used by caTissue Suite for IDP integration.

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.

catissue-participant-manager

Interfaces to participant manager and registration services to share registration information with other applications.

catissue-print-service

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

catissue-security-manager

caTissue Suite uses Common Security Module (CSM) software to accomplish the security requirements. caTissue Security Manager is an extention to CSM API addressing caTissue suite needs.

catissue-simple-query

Metadata driven mechanism to provide "simple query" functionality in caTissue Suite.

catissue-test

The caTissue Test contains a set of utilities to query and get results from each configured caTissue instance.

catissue-tools

The caTissue Tools contain several tools that integrate with the caTissue application.

catissue-utilities

caTissue Utilities include caGridLogger, Bioreposreport, caTissueCoreAPIExamples and caTissueLoader to help caTissue suite users.

catrip

caTRIP (Cancer Translational Research Information Platform) allows users to query across caGrid data services, join on common data elements and view their results in a user-friendly interface, in support of translational research.

cbiit-ahp3-software

null

CDR

caHUB CDR v6.3

CDR-Lite

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

cgr-bambino

Bambino: SNP caller and Alignment Viewer for Next Gen Data

cgr-pathOlogist

null

cgr-PoDA

null

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.

clinical-trials-search

null

cma

Cancer Molecular Analysis (CMA) portal allows integrative query and analysis of molecular data and clinical annotations.

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.

commonlibrary

Created as per request NCI-RITM0065579

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.

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.

common-security-module-docs

This repository holds documents for the Common Security Module (CSM) project under the NCIP channel. See https://github.com/NCIP/common-security-module for further information.

commons-module

caTissue Commons Module is used by the caTissue project under the NCIP channel.

cptac3

To support the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program

ctat-lncrna

null

ctat-metagenomics

null

ctat-mutations

null

ctat_slncky

Lncrna Detection - Slncky

ctms-commons

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

CURE

Software for "Collecting User Reported Experience" platform

digital-model-repository

Digital Model Repository is a web-based digital repository for the purpose of archiving, retrieving and exchanging cancer modeling modules and the data that link to it.

dwd

Distance Weighted Discrimination performs statistical corrections to reduce systematic biases in microarray data sets.

eagle

Environment And Genetics in Lung cancer Etiology (EAGLE) data portal allows capture and integrative query and analysis of epdemiology and microarray data.

edct-analytics

eDCT Analytics is a Web application that provide an easy and dynamic interface to navigate collected data through the eDCT Collector and enable ad-hoc data trend research and detection.

edct-cadsr-api-server

eDCT caDSR-API-Server Project integrates eDCT Form Builder with caDSR API and caDSR object cart.

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.

edct-common

eDCT Common project contains the common code used by eDCT Collector, eDCT Formbuilder and eDCT Analytics projects.

edct-formbuilder

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

gdc-docs

Official repository for GDC User Guides in Markdown format

geneconnect

GeneConnect is a mapping service that interlinks genomic identifiers.

gsid

The Global Specimen Identifier (GSID) Service is a NCI Enterprise Service. Global Specimen Identifer (GSID) is defined as the entity that contains a Globally Unique Idenitifer (UUID) and associated attributes that consists of a name value pair. A UUID is defined as a 16 byte identifier that is intended to be globally unique. There are 3 x 10^38 unique identifiers that can be obtained through the service.

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).

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.

ISAvalidator-ISAconverter-BIImanager

The ISAvalidator, ISA converter and BII data manager tools

ISAValidatorWS

Restful Webservice for Validation of ISATab files.

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.

i-spy

I-spy data portal allows integrative query and analysis of molecular data and clinical annotations.

keyword-search

caTissue Suite uses Keyword Search to provide searching and indexing capabilities.

labviewer

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

labviewer-docs

LabViewer-docs git repository contains relevant documents to LabViewer web application.

lexevs

The LexEVS Terminology Service.

lexevs-grid

caGrid Analytical and Data services for LexEVS.

lexevs-remote

A remote (RMI) access wrapper around LexEVS.

lexevs-service

A CTS2 Framework Service Plugin based on LexEVS

metadata-based-query

Metadata Based Query is used by the caTissue.

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.

nci-analysis-tools-web-presence

Contains both the framework for exposing R functions as web services and websites and the R code itself

nci-diff-CDISC

diff specific for CDISC reports

nci-edit-tab

evs' nci edittab plugin for the protege 5-based code

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.

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.

nci-ocr

null

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.

nci-protege5

evs umbrella project for protege 5-based editing software

nci-report-writer

The NCI EVS Report Writer is a web-based tool that allows users to generate reports from terminologies available through the LexEVS terminology server; it supports download and printing to a variety of file types and formats.

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-term-suggestion

The NCI Term Suggestion application is used both standalone and in the EVS terminology browsers to get community feedback and contributions to both NCI and EVS partner terminology products.

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.

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.

prot-express

ProtExpress supports proteomics experiment and protocol data management as well as eXperimental Archive (XAR) file creation.

psc

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

psc-docs

This is the documentation repository for the Patient Study Calendar (PSC) Project that is under the NCIP channel.

python-api

Python tools for accessing caCORE services that include pyCaCORE code generator, caBIO client (pyCaBIO) and EVS client (pyEVS)

qfive

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

quality-indicator-portal

Quality Indicator (QI) Portal allows users to submit and retrieve quality data for biospecimens.

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.

slncky

slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution.

stats-analysis

The purpose of Stats Analysis API is to allow programmatic and logical access to the underlying Data Mart via clinical genomic domain objects.

stats-analysis-commons

The Stats Analysis Commons API handles the messaging services between projects.

stats-analysis-server

The Stats Analysis Server performs on-the-fly statistical calculations for other applications.

stats-application-commons

The Stats Application Commons provides various utility functions such as mail server, scheduling, string manipulation, data download management, and caching functions.

taverna-grid

The taverna-grid repository is a Taverna Workbench plug-in to support invocation of caGrid 1.x services.

tcga-sandbox

null

tcga-sandbox-v1

null

tmt-catissue

Reporting and analysis of caTissue test scripts and results.

Trinity_CTAT

null

Trinity_CTAT_galaxy

Files needed for Galaxy tools used to run Trinity_CTAT workflows.

URI_Resolver

Resolves URIs for CTS2

visda

VISDA (VIsual Statistical Data Analyzer) is analytical tool for cluster modeling and visualization of microarray data.

webgenome

WebGenome is a web application for creating genomic plots of gene expression and copy number data.

webgenome-integration

Application to integrate WebGenome application with Rembrandt portal to allow plotting of array based data.

wustl-common-package

Wustl Common Package is used by the caTissue project.

wustl-common-utilities

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

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.