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.

• https://caintegrator2.nci.nih.gov/

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 (historical link)

• 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:

Molecular Analysis Tools Knowledge Center

Existing requests and resolution may be viewed at the caIntegrator2 GForge URL:

https://gforge.nci.nih.gov/tracker/?group_id=507   (historical link)

Documentation And Files
-----------------------

Links to all documentation and files can be found at:

caIntegrator 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/