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  1. 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...

  2. 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...

  3. 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...

  4. ITCR Monthly Teleconference September 4, 2015

    07 Oct 2015 | Contributor(s): Juli Klemm

     

  5. Brain Cancer Imaging Analytics

    02 Oct 2015 | Presentations | 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...

  6. HUBzero: A platform for dissemination and collaboration in Computational Science and Engineering

    07 Aug 2015 | Publications | Contributor(s): Michael McLennan, Rick Kennell

    The HUBzero cyberinfrastructure lets scientific researchers work together online to develop tools. Other researchers can then access the resulting tools using an ordinary Web browser and launch simulation runs on the national Grid infrastructure, without having to download or...

  7. UCSC Biomedical Evidence Graph Demonstration

    03 Jun 2015 | Presentations | Contributor(s): Josh Stuart, ellrott

    The BMEG demonstration includes the following elements: 1) Organization of crowd-source challenges to develop best-of-breed methods including an overview of current DREAM projects, living benchmarks; 2) Enabling cloud-ready methods for mass compute with examples of recently...

  8. Seven Bridges Cancer Genomics Cloud Pilot TCGA 2015 symposium workshop presentation

    23 May 2015 | Presentations | Contributor(s): Deniz Kural

    Basic and translational cancer research creates the need to disseminate, manage, and interpret large heterogeneous datasets. The volume and complexity of the data now routinely generated by high-throughput technologies has become too costly for individual laboratories and many research...

  9. The World of HUBzero

    11 Feb 2015 | Presentations | Contributor(s): Michael McLennan

    This part of a demo/presentation from the Force2015 conference giving you a 9 1/2 minute overview of the HUBzero platform and its capabilities - NCIP Hub is based on the HUBzero platform.[[Youtube(p_hpwoiXvEE,300,200)]]

  10. Video: Learn how TIES can help manage research resources

    16 Jan 2015 | Presentations | Contributor(s): Girish Chavan, Rebecca Crowley

    https://www.youtube.com/watch?v=EzjAo9LJ4tg  

  11. 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...

  12. QIN HUBzero update

    28 Oct 2013 | Teaching Materials | Contributor(s): Jayashree Kalpathy-Cramer

    presentation for the QIN EC meeting 10/21/2013

  13. HUBzero: A Web-based Platform for research, Education and Scientific Collaboration

    11 Sep 2013 | Presentations | Contributor(s): Michael McLennan

    Imagine an app store for scientists, engineers, and educators filled with simulation and modeling tools — not simple Java applets, but real research codes that tackle difficult problems and may require substantial computing power drawn from the Cloud. Imagine a new way of publishing...

  14. Overview on HUBzero - Building Scientific Communities Online

    03 Sep 2013 | Teaching Materials | Contributor(s): Michael McLennan

    This is a white paper/publication on the HUB and how one can build online communities using the HUBzero platform. See the tab on supporting documents for a video presentation.