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titleUseful Links

titleICR Active Working Groups
titlePrevious ICR Working Groups

The Integrative Cancer Research Workspace is producing modular and interoperable tools and interfaces that provide for integration between biomedical informatics applications and data. This will ultimately enable translational and integrative research by providing for the integration of clinical and basic research data. The Workspace is developing a software-engineered, well-documented and validated biomedical informatics toolset for use throughout the research community.

Additional information is also found on the Molecular Analysis Knowledge Center site.

Open Development and Community Projects Speaker Series

titleICR WS Teleconference Speakers

The Integrative Cancer Research (ICR) Workspace is hosting a series of speakers on various open development and community driven projects. While the applications may be of greatest interest to ICR, the conversations about success factors for these types of projects is of general interest to the caBIG community.

You are welcome to join us on the 2nd and 4th Wednesdays of each month from 2:00 – 4:00 pm ET. Teleconference information:
800-593-0616 passcode: 2927756.
Adobe connect:


June 22
BioPAX and GeneMANIA, Gary Bader (U. of Toronto)
I SPY/ Transcend, Sarah Davis (UCSF)

July 13
Protein Ontology, Cecilia Neomi Arighi (U. of Delaware)
Data standards and the Cardiovascular DAM at Duke University, Sal Mungal (Duke)

July 27
National Center for Biomedical Ontology - BioPortal, Trish Whetzel (Stanford)

August 10
POSTPONED: The Functional Genomics Data Society (FGED, formerly MGED), Chris Stoeckert (U. of Pennsylvania)]

Recent News

titlecaB2B releases v3.2

On behalf of the The caBench-to-Bedside (caB2B) development team at Georgetown University and caB2B Knowledge Center at Washington University , I am pleased to announce announced the availability of the caB2B v3.2. In this release caB2B's functionality has been expanded to better support complex queries that involve multiple services from multiple institutions such as caTissue Suite services at Prostate Cancer SPORE sites.
New features of the caB2B v3.2 include:

* Support queries that combine data across heterogeneous data services such as caTissue Core and Clinical Annotation Services

* Ability to group services to allow users to limit data combinations to a services from given institution or organization

* Ability to support login using NIH/NCI credentials

* Ability to manually load models using XMI files exported from UML authoring tools or domain model XML files that are available as part of caGrid service metadata

* Improved user interface navigation

* Improved default caB2B database with new service models and saved queries

* Improved server function including error handling, caching, security, and index service updates

The caB2B Web Application is available for the community's use at the following sites:

*  (Georgetown University instance).

*  (Washington University instance) and

*  (NCI instance).

We have released a new version of the NanoParticle Ontology(NPO). This version includes new terms that describe “scales of measurement” and nanomaterials. We made some modification to the nanomaterial branch and added new terms based on ISO terminology.

The NPO is now included in the NCI metathesaurus (NCIm), which can be accessed at NPO IN NCI METATHESAURUS.
The NCI metathesaurus contains about 3,600,000 terms from over 76 vocabularies, and these terms are mapped to about 1,400,000 biomedical concepts. Terms from multiple vocabularies that are mapped to a single biomedical concept allows the user to choose from the multiple vocabularies to annotate data. Simultaneously, this facilitates discovery of vocabularies unknown to the user. By the inclusion of NPO into the NCI metathesaurus, we expect that NPO accessibility and usage will be extended within the NCIm; NPO will add semantics into the NCIm; and that NCIm users will be able to take advantage of the knowledge provided by NPO.

The NCI term suggestion application allows for users to suggest terms for NPO. To suggest terms for NPO, you may use the NCI term suggestion application, available at NPO TERM SUGGESTION
titleNanoParticle Ontology
GenePattern 3.3.2 Released

The GenePattern development team is pleased to announce the release of GenePattern version 3.3.2. This release includes several major feature enhancements such as upload of large files to support RNA-seq analysis and the launching of datasets in the Integrative Genomics Viewer (IGV). To learn more about the enhancements and bug fixes in GenePattern 3.3.2, please visit the GenePattern landing page .

titleNew Molecular Analysis Tools Knowledge Center  Resources

The Molecular Analysis Tools Knowledge Center (MATKC) has created/updated several tutorials to assist users in using geWorkbench. Please visit geWorkbench Tutorials to learn more on Grid services, Multiple Probeset ID, Multiple Gene ID, Fold Change analysis, ARACNe, CNKB, ANOVA, Sequence Retriever, Volcano Plot, Color Mosaic, and SkyBase.

titlegeWorkbench v 2.2 released

The geWorkbench development team is pleased to announce the release of geWorkbench version 2.2.0.  This release includes more than 180 new features, enhancements and bug fixes. For a full list, see .

Teleconference Materials

The meeting Date is hyperlinked to the notes and hyperlinks in the Executive Summary are for specific presentations