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CRAVAT Introduction Video - Cancer Related Analysis of Variants
03 Dec 2014 | Teaching Materials | Contributor(s): Michael C Ryan
This video provides a brief overview of the CRAVAT web service(http://www.cravat.us/). CRAVAT provides annotation and analysis of cancer mutations. CRAVAT is free, very easy to use, and can handle large volumes of mutations.[[Youtube(xovmIy11Bcs)]]Please switch to 1080 resolution and watch...
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Databases on NCIP Hub
21 Nov 2014 | Teaching Materials | Contributor(s): Patrick Mulligan
Overview and demo of the database functionality on NCIP Hub. Further documentation on database functionality is included in the "Supporting Documentation" section.
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Extending 3D Slicer to support ground truth pathology tissue segmentation data for integrated pathology/radiology image analysis competitions.
06 Jan 2017 | Presentations | Contributor(s): Joel Haskin Saltz, Andrey Fedorov, Jayashree Kalpathy-Cramer
ITCR PI Monthly Meeting January 6, 2017 Collaborative project goal: Improve support in 3D Slicer for pathology imaging, generate high quality, well curated “ground truth” annotations, integrate key aspects of the Stony Brook ITCR project (FeatureDB) into the MGH project and...
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GenomeSpace Presentation
08 Feb 2016 | Presentations | Contributor(s): Michael Reich
GenomeSpace (http://www.genomespace.org) is a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes',...
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Getting Anal Cancer Screening & Participating in Research
22 Dec 2015 | Teaching Materials
Six minute video showing interviews of three HIV positive women telling their stories of living with HIV and choosing to participate in anal cancer screening as part of a clinical research project.
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Getting Started at the Standards Portal Pilot
27 Mar 2014 | Teaching Materials | Contributor(s): Denise Warzel, Ann Christine Catlin
The Standards Portal Pilot is now available! (Click the link for the portal home page.)Why use the standards portal? See more information about its genesis and use cases in a study conducted for the VCDE caBIG community here. If you are participating in the Pilot, please join the...
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Home Health Party: Colorectal Cancer Knowledge
16 Jul 2015 | Teaching Materials | Contributor(s): Kathy Briant
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Informatics to enable Routine Personalized Cancer Therapy (IPCT)
18 Feb 2014 | Presentations | Contributor(s): Elmer V. Bernstam, Funda Meric-Bernstam
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Informatics Tools for High-throughput Analysis of Cancer Mutations
15 Jan 2014 | Presentations | Contributor(s): Michael C Ryan, Rachel Karchin
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Integrated analysis of breast cancer cell lines reveals unique signaling pathways
16 Sep 2014 | Publications | Contributor(s): Laura M Heiser, Nicholas J Wang, Carolyn L Talcott, Keith R Laderoute, Merrill Knapp, Yinghui Guan, Zhi Hu, Safiyyah Ziyad, Barbara L Weber, Sylvie Laquerre, Jeffrey R Jackson, Richard F Wooster, Wen Lin Kuo, Joe W Gray, Paul T Spellman
AbstractBackgroundCancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which...
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Integrative Cancer Biology Program Datasets
26 Apr 2016 | Series | Contributor(s): Jonathan Bistline, Michael Reich
The NCI-ICBP promotes an integrative/systems approach to the study of cancer biology. The Program encourages scientists to study cancer as a complex biological system. Information gained from these studies are used to build reliable and testable predictive computation models of cancer processes...
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Introduction to the Trinity Cancer Transcriptome Analysis Toolkit
05 Feb 2015 | Teaching Materials | Contributor(s): Brian Haas, Aviv Regev, Bill Barnett
This short video provides an overview of our ITCR-funded effort to leverage RNA-Seq and de novo transcriptome assembly to assist researchers in studying cancer transcriptomes. Visit our NCGAS Trinity/Galaxy portal to access these compute...
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ITCR Monthly Teleconference September 4, 2015
07 Oct 2015 | Presentations | Contributor(s): Juli Klemm
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ITCR PI Meeting June 2014 Presentations
23 Jun 2014 | Series
Informatics Technology for Cancer Research (ITCR) Initiative held its Annual PI Meeting on June 12-13, 2014 in Rockville, MD. This series contains the presentations given at the meeting.
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LBL ICBP50 integrative genomic data
13 Nov 2014 | Downloads | Contributor(s): Joe Gray, Jonathan Bistline
From Joe Gray, Lawrence Berkeley National Laboratory. There are seventeen (17) files in this study: Affymetrix U133A gene expression data (icbp_u133a.gct) Affymetrix U133A gene expression data (ICBP_U133a.zip) Affymetrix splice junction exon-exon data (ICBP_Junction.zip) Affymetrix...
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Life after MOOCS: Online Science Education Needs a New Revolution
03 Feb 2017 | Presentations | Contributor(s): Phillip Compeau
ITCR Monthly PI Meeting, February 3, 2017 Presentation by Phillip Compeau (Carnegie Mellon U.)
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NCI Standard CRFs
15 Mar 2014 | Teaching Materials | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando
Working in conjunction with NCI has developed a collection of Standard Case Report Forms (CRFs) for use in developing new protocols. The project and its status are described here. The reuse of sections from standard CRFs helps to ensure that data collected in different studies is compatible and...
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NCIP Hub Dashboard Tutorial
15 Apr 2014 | Teaching Materials | Contributor(s): Lisa Mahoney
This is a short "how-to" video to familiarize users with the customizable dashboard on NCIP Hub.
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NCIP Hub QIN Workshop - March 3, 2015
19 Mar 2015 | Presentations | Contributor(s): Michael McLennan
Mike McLennan, director of HUBzero, presented an overview of basic NCIP Hub functionality to the QIN group on March 3, 2015. The presentation included an overview of the "hub" and HUBzero, and touched upon functionality such as projects, groups, resources and information sharing. The...
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Next-Generation Clustered Heat Maps (NG-CHM)
07 Oct 2015 | Presentations | Contributor(s): Weinstein John, Bradley Broom
Clustered Heat Maps (CHMs) have been referred to as the ubiquitous visual icons of post-genomic biology -- the most frequent type of visualization for large molecular profiling databases. However, “traditional” CHMs are static images -- a serious limitation. Accordingly, we have now...