Quantitative Image Informatics for Cancer Research (QIICR)

04 Apr 2014 | Presentations | Contributor(s): Andrey Fedorov, Ron Kikinis

So What Can We Do With Nano Informatics? – Leveraging Decision Analytic Tools

22 Jan 2015 | Presentations | Contributor(s): Igor Linkov, Matthew Bates

Jan 22, 2015 meeting                  Nanotechnology Working Group Matthew E. Bates & Igor Linkov Risk & Decision Science Team Environmental Laboratory, Engineer Research and Development Center, US Army...

Some Thoughts on Reproducibility

05 Dec 2014 | Presentations | Contributor(s): John Rumble

Nano WG December 4, 2014

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...

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...

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 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....

Support Access to NPO's Structure and Content

13 Aug 2015 | Presentations | Contributor(s): Michael Halper, Vladimir Ventura, Yehoshua Perl

•Abstraction Networks (“AbNs”) for Ontologies•Two example AbNs:–Area taxonomy–Partial-area taxonomy•BLUOWL: taxonomy-based software tool•Application to the NPO•Conclusions

TCGA Common Data Elements

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

TCGA Common Data ElementsTCGA version 2.6 CDEs are the standard elements that were used in validation of clinical data in the TCGA 2.6 data files. The data files are available for download at the Data Matrix. This resource page at the NCIP HUB presents the CDEs for easy search and discovery....

Text Mining, Data Mining and Molecular Dynamics Simulations for in Silico Design of PAMAM Dendrimers

17 Jun 2016 | Presentations | Contributor(s): Julio Facelli

Nano WG June 16, 2016 Text Mining, Data Mining and Molecular Dynamics Simulations for in Silico Design of PAMAM Dendrimers by Julio Facelli

The Digital Slide Archive

13 Jun 2017 | Presentations | Contributor(s): David A Gutman, Lee Cooper

Presentation at the 2017 Informatics Technology for Cancer Research Annual Meeting Advanced development of an open-source platform for web-based integrative digital image analysis in cancer.

The impact of engineered nanomaterials on aquatic species: ISA-TAB compatible dataset mined from literature (2007-2016)

13 Jun 2017 | Presentations | Contributor(s): Anastasios Papadiamantis

Nano WG presentation, June 8, 2017Primary scope of the project was to: Model the toxicity of engineered nanomaterials (ENMs) at multiple levels and design and create a database (DB) containing extracted peer-reviewed published toxicity dataAnalyse the extracted data and identify...

The NANoREG Toolbox for the safety assessment of nanomaterials

16 Jan 2018 | Presentations | Contributor(s): Paula Jantunen

Presentation for the Nano WG on January 11, 2018 by Paula Jantunen,  The European Commission’s science and knowledge service Joint Research Centre NANOoREG Toolbox supports the framework by identifying & inventorying tools for the different steps and options of...

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...

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

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...