Data Collection from the Nanotoxicology Literature Using ISA-TAB-Nano

21 Jan 2016 | Presentations | Contributor(s): Richard Liam Marchese Robinson

Nano WG meeting January 21, 2016 This is an updated version of the talk originally delivered at the CompNanoTox2015 conference. [1] Marchese Robinson, R.; Richarz, A.N.; Cassano, A.; Cronin, M.T.D; Rallo, R. (2015): Data Collection from the Nanotoxicology Literature Using ISA-TAB-Nano. FigShare....

Summary of the 2015 Epigenetic Engineering for Cancer Workshops

22 Dec 2015 | Publications | Contributor(s): Tony Dickherber

This document provides a general summary of the 2 virtual workshops held in Fall of 2015 to explore the suitability of epigenetic engineering tools to specifically modify epigenetic loci to study and/or treat cancer.

Materials Science Data Management Initiatives at NIST

17 Dec 2015 | Presentations | Contributor(s): Robert J. Hanisch

Nano WG December 17, 2015   •NIST is a national and world resource for fundamental data •Access should be easy and open –With regard to IP and privacy issues •As our nation’s standards organization… –NIST should be a leader in national and...

The Open Scholarship Initiative (OSI)

17 Dec 2015 | Presentations | Contributor(s): Glenn Hampson

Nano WG meeting November 19, 2015. : "What should the future of scholarly publishing look like? How about open access? Who should decide? Can journals become more affordable and accessible? Will journals continue to serve as the primary means of communicating research? Can institutional...

Nanomaterial Registry Update

22 Oct 2015 | Presentations | Contributor(s): Karmann Mills, Anthony Hickey, Alexander Tropsha

Nano WG weekly meeting October 22,2015

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...

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...

Introduction to the Trinity Cancer Transcriptome Analysis Toolkit

05 Feb 2015 | Teaching Materials | Contributor(s): Brian Haas, Aviv Regev, Bill Barnett

This short video provides an overview of our ITCR-funded effort to leverage RNA-Seq and de novo transcriptome assembly to assist researchers in studying cancer transcriptomes.  Visit our NCGAS Trinity/Galaxy portal to access these compute...

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  

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...

Multiclass cancer diagnosis using tumor gene expression signatures

10 Nov 2014 | Downloads

Experiment Description:    The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical...

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...

Getting Started at the Standards Portal Pilot

27 Mar 2014 | Teaching Materials | Contributor(s): Denise Warzel, Ann Christine Catlin

The Standards Portal Pilot is now available! (Click the link for the portal home page.)Why use the standards portal? See more information about its genesis and use cases in a study conducted for the VCDE caBIG community here. If you are participating in the Pilot, please join the...

Standards Portal CRFs Complete View

19 Mar 2014 | Downloads | Contributor(s): Denise Warzel, Sumudinie fernando, Ann Christine Catlin

This DataView resource page is for the Standards Portal CRFsUse this DataView to browse,search, explore and download the complete set of columns for NCI case report form standards at the Hub. These CRFs were brought to the Hub for clarification, discussion and discovery. They were assembled by...

Standards Portal CDEs Common Data Fields

19 Mar 2014 | Downloads | Contributor(s): Denise Warzel, Sumudinie fernando, Ann Christine Catlin

This DataView is for the Common Data Fields of the Standards Portal CDEsUse this DataView to browse, search, explore and download the essential set of columns for NCI common data elements standards at the Hub. These CDEs were brought to the Hub for clarification, discussion and discovery. They...

Standards Portal CRFs Common Data Fields

19 Mar 2014 | Downloads | Contributor(s): Denise Warzel, Sumudinie fernando, Ann Christine Catlin

This DataView is for the Common Data Fields of the Standards Portal CRFsUse this DataView to browse, search, explore and download the essential set of columns for NCI case report form standards at the Hub. These CRFs were brought to the Hub for clarification, discussion and discovery. They were...

Why Use the Standards Portal at the Hub?

19 Mar 2014 | Teaching Materials | Contributor(s): Denise Warzel, Sumudinie fernando, Ann Christine Catlin

The materials attached to this page were provided by Baris Suzek, who at the time was the Informatics Project Lead at the Innovation Center for Biomedical Informatics at Georgetown University School of Medicine. He conducted a study for the caBIG VCDE community to help clarify some of the...

Standards Portal Vocabulary DataView

15 Mar 2014 | Teaching Materials | Contributor(s): Sherri de Coronado, Denise Warzel, Ann Christine Catlin, Sumudinie fernando

The DataView for terminology referenced/used by the CDEs and CRFs currently contained in the Standards PortalThe DataView on this resource page can be used to browse, search, explore and download the NCI concepts for vocabulary referenced by the CDEs and CRFs uploaded to the Standards Portal....

Standards Portal CDEs Complete View

15 Mar 2014 | Teaching Materials | Contributor(s): Denise Warzel, Ann Christine Catlin, Sumudinie fernando

This DataView on this resource page is used to explore the Standards Portal CDEsUse the DataView provided on this resource page to navigate, browse, search, explore and download the complete set of columns for NCI common data elements standards at the Hub. These CDEs are brought to the Hub for...