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  1. The World of HUBzero

    11 Feb 2015 | 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)]]

  2. Three transplantable mouse mammary tumor models of human breast cancer were used to assess the effects of fixation on morphology and the preservation of 4 breast antigens (ER, PR, Ki67, Her2).

    04 Jun 2014 | Publications | Contributor(s): Neil Hubbard

    Quantitative Image Analysis (QIA) of digitized whole slide images for morphometric parameters and immunohistochemistry of breast cancer antigens was used to evaluate the technical reproducibility, biological variability, and intratumoral heterogeneity in three transplantable mouse mammary tumor...

  3. Tips for creating Standards Group Pages

    22 May 2014 | Teaching Materials | Contributor(s): Denise Warzel

    The Standards Portal offers a way to organize dsicussions and resources related to a set of standards. The organizing construct can be either a community interested in sharing data or using common tools, or by a particular type of standard, for example demographics or biomarkers. An example of a...

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

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

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

  5. Tools to Analyze Morphology and Spatially Mapped Molecular Data

    03 Oct 2014 | Presentations | Contributor(s): Joel Saltz

  6. Transcriptome assembly for genetic and functional analysis of cancer

    07 Mar 2014 | Presentations | Contributor(s): Aviv Regev, Brian Haas

  7. Transitioning to Predictive Analysis for Nanoparticle Biocorona Studies

    14 May 2019 | Presentations | Contributor(s): Korin Wheeler

    Nano WG April 18, 2019: Proteins adsorbed to nanomaterials in a biological environment mediate cellular recognition, uptake, and toxicity of nanomaterials. Here, Dr. Korin Wheeler presents the development of experimental methods to characterize this population of proteins (also...

  8. Translational Cancer Imaging

    18 Apr 2014 | Presentations | Contributor(s): Tony Ng, David Hawkes, Shonit Punwani

  9. Trinity: RNA-Seq De novo Assembly Application

    30 Jun 2015 | External Applications | 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...

  10. Trinity: Transcriptome assembly for genetic and functional analysis of cancer

    23 Jun 2014 | Presentations | Contributor(s): Aviv Regev, Brian Haas, Bill Barnett

    ITCR PI meeting presentation.Note: A reminded that these include unpublished results and hence should not be shared further.

  11. Tufts Gene Expression Data for Low Dose Radiation Experiments

    13 Nov 2014 | Downloads | Contributor(s): Lynn Hlatky, Edward Rietman, Jonathan Bistline

    Expression signatures from low dose radiation exposure of various types of tissues. There are eight (8) files in this study: 1-7. Gene expression of cell lines exposed to low-dose radiation ( to 8. Sample Annotation (ICBP_Data_Upload_Samples.xlsx)...

  12. U24 KickOff Steering Committee Meeting 022614

    12 Mar 2014 | Downloads | Contributor(s): Rebecca Crowley

    Kick of For Steering Committee - explains grant and discusses process for developing the TIES Cancer Research Network

  13. 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...

  14. UCSC Xena System

    07 Mar 2014 | Presentations | Contributor(s): Jingchun Zhu

  15. Understanding Colorectal Cancer to Protect our Communities

    24 Nov 2015 | Teaching Materials | Contributor(s): NCI

    This is a teaching material originally developed by NCI. 

  16. US-EU Nanoinformatics Roadmap Update

    27 Jul 2016 | Presentations | Contributor(s): Frederick C. Klaessig

    US-EU Nanoinformatics Roadmap Update for the Nano WG on July 28, 2016

  17. Values Of Precision and the Societal Implications Of Data Readiness Levels

    19 Jun 2014 | Presentations | Contributor(s): Sharon Ku

  18. Vanderbilt PC9 cell line exposed to varying concentrations of erlotinib

    13 Nov 2014 | Downloads | Contributor(s): Vito Quaranta, Shawn Garbett, Jonathan Bistline

    Histone H2B labeled PC9 NSCLC cell line exposed to varying concentrations of erlotinib.  There are twenty-five (25) files in this study: 1-24. Cell Motility Movies (*.mov) 25. Sample Annotation (2011-06-13_PC9_erlot_plate_map.txt) These datasets have been exported from the Broad...

  19. Vanderbilt Single-cell motility data

    13 Nov 2014 | Downloads | Contributor(s): Vito Quaranta, Shawn Garbett, Jonathan Bistline

    All epithelial-derived cell lines (MCF10A, AT1, and CA1d) were plated on laminin-332, and incubated under either "mild" or "harsh" microenvironmental conditions (full tissue culture media vs. deprived media (-fetal bovine serum, -EGF), respectively). Single-cell motility was...

  20. Vanquishing Cancer Through Genomics

    23 Jun 2014 | Presentations | Contributor(s): Louis Staudt

    ITCR PI meeting presentation