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Tags: ITCR

All Categories (1-20 of 49)

  1. 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.

  2. 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 

  3. 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

  4. 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.)

  5. 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...

  6. Post #1111

    Collections | 16 Nov 2016 | Posted by Mervi Heiskanen

    https://nciphub.org/groups/itcr/collections/itcr-training-assets

  7. ITCR Active Portfolio 2016

    19 Oct 2016 | Datasets | Contributor(s):

    By Mervi Heiskanen

    National Cancer Institute

    ITCR Active Grants October 2016

    https://nciphub.org/publications/45/?v=1

  8. 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.

  9. UCSC Xena Basic Tutorial

    Collections | 07 Jul 2016 | Posted by Mary Goldman

    https://nciphub.org/groups/itcr/collections/itcr-training-assets

  10. 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

  11. 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.  

  12. Next-Generation Clustered Heat Maps (NG-CHM)

    Collections | 24 Mar 2016 | Posted by Mervi Heiskanen

    https://nciphub.org/groups/itcr/collections/itcr-training-assets

  13. MeV: Multiexperiment Viewer

    Collections | 23 Mar 2016 | Posted by Mervi Heiskanen

    https://nciphub.org/groups/itcr/collections/itcr-training-assets

  14. 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',...

  15. 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...

  16. 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...

  17. 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...

  18. ITCR Monthly Teleconference September 4, 2015

    07 Oct 2015 | | Contributor(s):: Juli Klemm

     

  19. 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...

  20. 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...