Release Name: 1.0
Notes:
Notes:
Release Notes
=============
#Product:# caIntegrator2
#Version:# 1.0
#Date:# Oct 2009
Contents
--------
1. Introduction
2. Release History
3. Anticipated Releases
4. Features and Defects Addressed in this Release
5. Known Issues/Defects
6. Bug Reports, Feature Requests and Support
7. Documentation and Files
8. NCICB Web Pages
Introduction
---------------------------
caIntegrator2 is a web-based software package that allows researchers to set up custom, caBIG®-compatible web portals to conduct integrative research, without requiring programming experience. These portals bring together heterogeneous clinical, microarray and medical imaging data to enrich multidisciplinary research.
Using caIntegrator2, researchers can execute, save and share queries to identify and collect many types of data, combining clinical information with genetic and genomic data to enable multidimensional analysis. caintegrator2 uses caGrid analytical services such as GenePattern and BioConductor to perform analysis on the integrated study data, including clinical survival data.
Release History
------------------------
- caIntegrator2 v1.0 – Oct 2009
Anticipated Releases
------------------------ - caIntegrator2 v1.1 – Dec 2009
Features and Defects Addressed in this Release
-----------------------------------------------
This release is the first release of caIntegrator2
Highlights of caIntegrator2 v1.0 are:
- Deploy a study using the following data types
Clinical data as spreadsheet
Gene Expression Data from caArray (2.3.0 or higher version)
CopyNumber Data from caArray (2.3.0 or higher version
Image Mapping with NBIA (4.2.2 or higher version)
Image Annotations as spreadsheet
- Integration with caDSR for mapping to well defined data types
- Run and Save queries across clinical, genomic and image annotations.
- Integration with caBIO to perform queries on genes
- Integration with GenePattern grid to perform the following analysis
Comparative Marker Selection
Principal Component Analysis
GISTIC Analysis
- Integration with GenePattern (3.1.1) as a Web client
- Perform analysis like KM-plot, Gene Expression plots and Fold Change Calculations.
- Platforms Supported include
Affymetrix geneExpression
Affymetrix SNP
Agilent Gene Expression
Agilent CopyNumber (aCGH)
Known Issues/Defects
------------------------
See the GForge tracker for existing open defects, community requests,
resolutions and feature requests. The following issues are
highlighted.
https://gforge.nci.nih.gov/tracker/?group_id=507
- Copynumber/GISTIC issues
Bug Reports, Feature Requests, And Support
------------------------------------------
Send email to ncicb@pop.nci.nih.gov to request technical support. To
report a bug or request a new feature, please visit the Molecular Analysis Tools
Knowledge Center resources at:
https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page
Existing requests and resolution may be viewed at the caIntegrator2 GForge URL:
https://gforge.nci.nih.gov/tracker/?group_id=507
Documentation And Files
-----------------------
Links to all documentation and files can be found at:
https://wiki.nci.nih.gov/display/caIntegrator2/caIntegrator2+Wiki
NCICB Web Pages
---------------
- 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/