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  1. A Brief History of OpenTox

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    25 Jun 2015 | Presentations | Contributor(s): Barry Hardy

    Nano WG June 25, 2015 The history and challenges of OpenTox developments and the potential of its community, framework and principles applied to advancing safety assessment goals.  

  2. CRAVAT - Cancer-Related Analysis of Variants Toolkit

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    23 Jun 2015 | External Applications | 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...

  3. Tools for Creation of Integrated Data Repository for Cancer Research

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    16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang

    Admin Supplement Proposal Parent Projects: DeepPhe (PIs: Savova and Jacobson) caCDE-QA (PI: Jiang)

  4. A Semantic Web-based Quality Assurance Tool for Cancer Study Common Data Elements

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    16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang

    A poster presentation from the caCDE-QA project (PI: Jiang)  

  5. Building the Knowledgebase of Biology using Citizen Science

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    12 Jun 2015 | Presentations | Contributor(s): Andrew Su

    Andrew Su discusses Mark2Cure and how to build a knowledgebase of biology using citizen science.

  6. Notes from the ITCR Annual Meeting May 27-28, 2015

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    10 Jun 2015 | Downloads | Contributor(s): Ishwar Chandramouliswaran, Juli Klemm

    Notes from the ITCR Annual Meeting May 27-28, 2015

  7. UCSC Biomedical Evidence Graph Demonstration

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    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. Informatics for Routine Personalized Cancer Therapy Demo (ITCR meeting UCSD 5.2015)

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    01 Jun 2015 | Presentations | Contributor(s): Elmer Bernstam, funda meric-bernsatm

    Attached please find screenshots of the resources that we demonstrated at the ITCR meeting in San Diego. This resource is intended to help clinicians understand and leverage molecular profiling to choose treatments for their patients. We are also working on automating literature and clinical...

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

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    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...

  10. Petabyte-Scale Cancer Genomics in the Cloud - TCGA Symposium 2015 Poster Presentation

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    15 May 2015 | Presentations | Contributor(s): Brandi Davis Dusenbery, Zeynep Onder, Devin Locke, Kate Blair, Deniz Kural

    The advent of next generation sequencing has transformed our ability to generate genomic data. Today, cancer researchers have access to petabytes of multi-dimensional information from thousands of patients. However, analysis of this information only becomes more challenging as the amount of data...

  11. Role of HER4 in Neuroblastoma

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    07 May 2015 | Presentations | Contributor(s): Arianexys Aquino-Lopez

    Neuroblastoma (NBL) is the 4th most common pediatric tumor. Globally it constitutes 8-10% of all childhood cancers and is responsible of approximately 15% of all pediatric cancer deaths. It remains a challenge for pediatric oncologists, since long term survival for disseminated NBL is only less...

  12. Molecule & Particle Differentiation Using Electrophoresis

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    28 Apr 2015 | Presentations | Contributor(s): Frederick C. Klaessig, Sharon Ku

    Nano WG April 16, 2015

  13. caCDE-QA: A quality assurance platform for cancer study common data elements

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    26 Mar 2015 | Presentations | Contributor(s): Guoqian Jiang

    This is a presentation about an overview of a NCI ITCR U01 project - caCDE-QA: A quality assurance platform for cancer study common data elements (PI, Guoqian Jiang, Mayo Clinic). The goal of the project is to design, develop and evaluate an integrative platform known as caCDE-QA that implements...

  14. Software Discovery Index Workshop Report

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    25 Mar 2015 | Publications | Contributor(s): Vivien Bonazzi, Phil Bourne, Steven Brenner, Robin Brown, Ishwar Chandramouliswaran, Jennifer Couch, Sean Davis, Leslie Derr, Asif Dhar, Luke Dunlap, Kevin Eliceiri, Leigh Finnegan, Ian Fore, Melissa Haendel, Martin Hammitzsch, Tram Huyen, Daniel S. Katz, Mike Kellen, David Kennedy, Jennie Larkin, Jennifer Lin, Peter Lyster, Ron Margolis, Gabor Marth, Maryann Martone, Michael McLennan, Martin Morgan, Francis Ouellette, Vinay Pai, Andreas Prlic, Will Schroeder, Michael Sherman, Heidi Sofia, James Taylor, Kaitlin Thaney, Chris Wellington, Owen White

    The National Institutes of Health (NIH), through the Big Data to Knowledge (BD2K) initiative, held a workshop in May of 2014 to explore challenges facing the biomedical research community in locating, citing, and reusing biomedical software. The workshop participants examined these issues and...

  15. Nanoinformatics Workshop 2015

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    23 Mar 2015 | Presentations | Contributor(s): Mark Tuominen, Mervi Heiskanen

    Nano WG March 19, 2015.

  16. NCIP Hub QIN Workshop - March 3, 2015

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    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...

  17. MC-GPU at Google Code

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    12 Mar 2015 | External Applications | Contributor(s): Andreu Badal

    Link to MC-GPU at Google Code

  18. Why in the world do we need a nanomaterials description system – How CODATA and VAMAS answers that question

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    12 Mar 2015 | Presentations | Contributor(s): John Rumble

    Nano WG March12, 2015

  19. mitoticapp

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    10 Feb 2015 | Tools | Contributor(s): Qi Gong

    mitotic figure counter

  20. DWIConvert

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    04 Mar 2015 | External Applications | Contributor(s): Vince Magnotta, Hans Johnson, Joy Matsui, Kent Williams, Mark Scully, Xiaodong Tao

    Converts diffusion weighted MR images in dicom series into Nrrd format for analysis in Slicer. This program has been tested on only a limited subset of DTI dicom formats available from Siemens, GE, and Phillips scanners. Work in progress to support dicom multi-frame data. The program parses dicom...