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Release Name: 1.0.1
Notes:
Release Notes
=============

#Product:# caIntegrator2
#Version:# 1.0.1
#Date:# Jan 11 2010

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, and save 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 v1.0.0 – Oct 2009
  • caIntegrator2 v1.0.1 – Jan 2010
    Anticipated Releases
    ------------------------
  • caIntegrator2 v1.1 – 2010

Highlights of caIntegrator2 v1.0.1 are:
-----------------------------------------------

  • Addition of a new Visible parameter for Study Managers to select how data annotation is shown to Study Investigators.
  • Study Investigators can create Lists of Genes and save them for use in Analysis workflows.
  • A new capability for searching pathway data in caBio, and for creating gene lists from pathway search results.
  • A new capability for searching gene symbols in caBio, and for creating gene lists from search results.
  • A new capability for using multiple keywords in all caBio searches.
  • Corrected links for support and contact.
  • Interface to GenePattern grid-based modules now provides a link for downloading GCT and CLS files.
  • Option to upgrade to newer versions of caIntegrator2 without removing existing study data and user data.
  • Study Managers can now add customizable external links, which are displayed as part of the study.

Features and Defects Addressed in this Release
-----------------------------------------------
ID Summary

21941 Perform Analysis - caBio integration - USBAT search with multiple keywords.%%%
22301 USBAT save lists of genes.%%%
24104 USBAT specify a search on a partial HUGO symbol and get partial matches.%%%
24415 USBAT - Set visibility of each annotation field in the clinical data file%%%
24427 Manage Platforms: add spinner icon while existing platforms table is being loaded.%%%
24512 Changes to the User Registration Forms%%%
21654 Perform Analysis - Get Gene Symbols - 2 USBAT Search Pathways in cabio.%%%
24390 Cannot Sort Image Data in Clinical Query with Clinical and Image Results Type%%%
24358 Redundant Error Messages for Bad Clinical Data Sources File%%%
24367 Pressing Enter on caDSR Search input box should start search%%%
24146 NBIA Server Grid URL is hard to edit%%%
24268 Study Management: If the creator isn't the user running the asynchronous jobs it will not auto update.%%%
23789 Edit Copy Number Data Configuration: usage of 'cnchp' files must be clearly documented.%%%
24239 Need separation between Gene Expression and Copy Number data in Study Summary Page%%%
24279 Support and Contact links are broken.%%%
24338 Session Timeout Not Working%%%

Known Issues/Defects
------------------------

1. caIntegrator2 1.0 will not work as expected with Firefox 3.5 release. When using Firefox 3.5, the user will experience random blank pages. If it occurs, reloading the page using the Reload button will redisplay the page.%%%
2. A Study with copyNumber data from an Agilent platform is not fully tested.%%%
3. A Study with copyNumber data from Affymetrix is fully tested for only 100K platforms.%%%
4. GISTIC analysis of Agilent array data produces erroneous results because Level 2 data is not available in the AGILENT_RAW_TXT files in caArray.%%%
5. Platform creation for copyNumber for 100K Affymetrix expects the user to Add/upload two 50K annotation files while creating the platform. The same rule applies to other Affymetrix Copy Number platforms - for example 500K etc.%%%
6. The “Delete” platform feature may produce a timeout error while it is executing. If a timeout is experienced, don’t click again on the Delete link, as multiple clicks on “Delete” platform can create performance issues. Refresh the Manage Platforms page to check to see if the deletion is complete. The time needed to Delete a platform is roughly the same time need to load the same platform.%%%

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)

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
---------------

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