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)]]

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...

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...

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)

Tools to Analyze Morphology and Spatially Mapped Molecular Data

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

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...

Translational Cancer Imaging

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

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...

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 (5727049056.zip to 7196780010.zip) 8. Sample Annotation (ICBP_Data_Upload_Samples.xlsx)...

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

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...

Understanding Colorectal Cancer to Protect our Communities

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

This is a teaching material originally developed by NCI. 

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

Values Of Precision and the Societal Implications Of Data Readiness Levels

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

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...

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...