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The Digital Slide Archive
13 Jun 2017 | | Contributor(s):: David A Gutman, Lee Cooper
Presentation at the 2017 Informatics Technology for Cancer Research Annual Meeting Advanced development of an open-source platform for web-based integrative digital image analysis in cancer.
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Activities to Promote Technology Research Collaborations (APTRC) PA-17-143 Pre-Application Webinar
24 Feb 2017 | | Contributor(s):: Juli Klemm, Tony Dickherber
Pre-application seminar held February 24, 2017 for FOA PA-17-143
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LesionTracker: Open-source extensible web viewer for oncology research and clinical trials
Collections |
03 Feb 2017 |
Posted by Gordon Harris
https://nciphub.org/groups/itcr/collections/itcr-training-assets
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Life after MOOCS: Online Science Education Needs a New Revolution
03 Feb 2017 | | Contributor(s):: Phillip Compeau
ITCR Monthly PI Meeting, February 3, 2017 Presentation by Phillip Compeau (Carnegie Mellon U.)
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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 | | 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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Post #1111
Collections |
16 Nov 2016 |
Posted by Mervi Heiskanen
https://nciphub.org/groups/itcr/collections/itcr-training-assets
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Providing National Cyberinfrastructure to Biologists, esp. Genomicists
02 Sep 2016 | | Contributor(s):: Tom Doek, Mervi Heiskanen
National Center for Genome Analysis Support (NCGAS) provides access to High Performance Computing resources for biologists. NCGAS also maintains a curated set of applications and Galaxy instances of their software, as well as provides bioinformatics expertise.
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UCSC Xena Basic Tutorial
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07 Jul 2016 |
Posted by Mary Goldman
https://nciphub.org/groups/itcr/collections/itcr-training-assets
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ITCR 2016 Annual PI Meeting Presentations
ITCR 2016 Annual Meeting
Notes are available here
Posters are available here
Participant List is available here (ITCR Group Members Only)
Day One
Welcome: Juli Klemm and Aviv...
https://nciphub.org/groups/itcr/wiki/AgendaandPresentations
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An Extensible and Scalable Knowledge System Architecture for Cancer Research
06 May 2016 | | Contributor(s):: Daniel Crichton
ITCR May 2016 PI meeting presentation on development of an advanced knowledge system to capture, share and support reproducible analysis from the biomarker data results.
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Next-Generation Clustered Heat Maps (NG-CHM)
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24 Mar 2016 |
Posted by Mervi Heiskanen
https://nciphub.org/groups/itcr/collections/itcr-training-assets
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MeV: Multiexperiment Viewer
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23 Mar 2016 |
Posted by Mervi Heiskanen
https://nciphub.org/groups/itcr/collections/itcr-training-assets
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GenomeSpace Presentation
08 Feb 2016 | | 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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Pathology Image Informatics Platform for visualization, analysis and management
07 Oct 2015 | | Contributor(s):: Metin Gurcan, Anant Madabhushi, Anne Martel
This multi-institutional proposal seeks to expand on an existing, freely available pathology image viewer (Sedeen Image Viewer) to create a pathology informatics platform (PIIP) for managing, annotating, sharing, and quantitatively analyzing digital Pathology Imaging (DPI) data. Sedeen has become...
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Next-Generation Clustered Heat Maps (NG-CHM)
07 Oct 2015 | | 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...
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Open source diffusion MRI technology for brain cancer research
07 Oct 2015 | | Contributor(s):: Lauren O\'Donnell
Using measurements of water diffusion, dMRI can give unique insights into the microstructure and cellular orientation of tissues. There is a growing awareness in the neurosurgery community that diffusion models must move beyond the current clinical standard of the diffusion tensor for better...
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ITCR Monthly Teleconference September 4, 2015
07 Oct 2015 | | Contributor(s):: Juli Klemm
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Brain Cancer Imaging Analytics
02 Oct 2015 | | Contributor(s):: Christos Davatzikos
The transition of oncologic imaging from its “industrial era” to it is “information era” demands analytical methods that 1) extract information from this data that is clinically and biologically relevant; 2) integrate imaging, clinical, and genomic data via rigorous...
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Trinity: RNA-Seq De novo Assembly Application
30 Jun 2015 | | Contributor(s):: Grabherr MG, Brian Haas, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Di Palma F, Birren BW, Nusbaum C, Lindblad-toh K, Friedman N, Regev A
Quick Guide for the ImpatientTrinity assembles transcript sequences from Illumina RNA-Seq data.Download Trinity here.Build Trinity by typing make : ; in the base installation directory.Assemble RNA-Seq data like so:Trinity --seqType fq --left reads_1.fq --right reads_2.fq...
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CRAVAT - Cancer-Related Analysis of Variants Toolkit
23 Jun 2015 | | Contributor(s):: Rachel Karchin, Michael C Ryan
cravat is a bioinformatics pipeline : ; that performs high-throughput cancer-related analysis of variants. it : ; utilizes three applications: CHASM (Cancer-Specific Analysis of Somatic Mutations), VEST and SVN-Get. More information on these tools is available at CHASM Software.Release...