Notes:
caGWAS Release Name: 1.0
Notes:
Release Notes
=============
#Product:# caIntegrator-caGWAS
#Version:# 1.0
#Date:# February 2008
Contents
--------
1. Introduction
2. Release History
3. Features
4. Known Issues/Defects
5. Bug Reports, Feature Requests, and Support
6. Documentation and Files
7. NCICB Web Pages
Introduction
---------------------------
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.
* https://caintegrator.nci.nih.gov/cgems
Release History
------------------------
* caGWAS v1.0 -- February 2008
Features
------------------------
This release represents a new generation of the caIntegrator’s GWAS
portal. It is build upon the CGEMS study use cases but has been
generalized to be platform and disease agnostic
Highlights of caGWAS 1.0 include:
Following the principals of caBIG, caGWAS APIs and web portal
provide:
* A semantically annotated domain model, database schema with
sample data, seasoned middleware, APIs, and web portal for GWAS
data;
* Platform and disease agnostic CGOM-caGWAS model and associated
APIs;
* The opportunity for developers to customize the look and feel
of their GWAS portal;
* A foundation of open source technologies;
* A well-tested and performance-enhanced platform, as the same
software is being used to house the CGEMS data portal at
https://caintegator.nci.nih.gov/cgems;
* Accelerated analysis of results from various biomedical
studies; and
* A single application through which researchers and
bioinformaticians can access and analyze clinical and
experimental data from a variety of data types, as caGWAS objects
are part of the CGOM, which includes microarray, genomic,
immunohistochemistry, imaging, and clinical data.
* Java API and Grid Service
The Java and caGRID APIs for caGWAS were generated using caCORE SDK
version 3.2.1 and caGRID Introduce toolkit version 1.1
* Installation
caGWAS 1.0 provides a simple ant based installation script and has been
tested on 64 bit, 32 bit and Windows XP platforms. The installation
also includes a mySQL dump file with sample GWAS data to allow
application validation.
Known Issues/Defects
------------------------
See the GForge tracker for the latest use cases, existing open defects,
community requests, resolutions and feature requests. The following
issues are highlighted.
https://gforge.nci.nih.gov/tracker/?group_id=305
[#10743] If you select any item from “Population” only the query
doesn’t bring any records.
[#11721] LSD - Exception/Error in server.log file for browse data query
- results still displayed correctly
Bug Reports, Feature Requests, And Support
------------------------------------------
Send email to ncicb@pop.nci.nih.gov to request support or report a bug
or request a new feature. Existing requests and resolution may be
viewed at the caGWAS GForge URL:
* https://gforge.nci.nih.gov/tracker/?group_id=379
Documentation And Files
-----------------------
Links to all documentation and files can be found at:
https://gforge.nci.nih.gov/projects/cagwas/
NCICB Web Pages
---------------
* caIntegrator Home page http://caintegrator-info.nci.nih.gov/
* The NCI Center for Bioinformatics, http://ncicb.nci.nih.gov/
* NCICB Application Support, http://ncicb.nci.nih.gov/NCICB/support
* NCICB Download Center, http://ncicb.nci.nih.gov/download/
Changes:
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