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...

Data Acquisition Working Group

21 Apr 2014 | Presentations | Contributor(s): Tom Chenevert, Paul Kinahan

DA-WG Update on PET-CT and DWI MRI

Dataset Curation, Assessment of their Quality, and Prediction Model Developments for Safe and Sustainable Nanotechnology (S2NANO)

29 Nov 2018 | Presentations | Contributor(s): Tae Hyun Yoon

Nano WG November 29, 2018: Tae Hyun Yoon, Prof./CEO/Ph.D., Yoon Idea Lab. Co. Ltd. & Hanyang University In this presentation, I will introduce our recent research outcomes from S2NANO: PredictNANO project, which aimed to bridge the nanosafety knowledge gaps between R&D...

Dissolution as a Paradigm in Regulating Nanomaterials

16 Aug 2017 | Presentations | Contributor(s): Frederick C. Klaessig

Nano WG presentation, August 10, 2017 Themes: • Dissolution as a decision criterion • Analogies to ζ-potential & VSSA • Relation to nanoform & nanoscale form • Dissolution kinetics and artifacts • ASTM particle ontology & Nanoinformatics Roadmap...

European Chemical Agency's work to implement REACH regulation for nanomaterials

04 May 2017 | Presentations | Contributor(s): Frank Le Curieux

Nano WG presentation on May 4, 2017.  REACH = Registration, Evaluation, Authorisation (& restriction) of Chemicals aims to ensure a high level of protection of human health and the environment while enhancing competitiveness and innovation. Nano materials are covered by...

Extending 3D Slicer to support ground truth pathology tissue segmentation data for integrated pathology/radiology image analysis competitions.

06 Jan 2017 | Presentations | Contributor(s): Joel Haskin Saltz, Andrey Fedorov, Jayashree Kalpathy-Cramer

ITCR PI Monthly Meeting January 6, 2017 Collaborative project goal: Improve support in 3D Slicer for pathology imaging, generate high quality, well curated “ground truth” annotations, integrate key aspects of the Stony Brook ITCR project (FeatureDB) into the MGH project and...

FAIR for NanoSafety: where do we stand?

05 Apr 2019 | Presentations | Contributor(s): Egon Willighagen

Nano WG April 4, 2019 Findable, Accessible, Interoperable, Reusable (FAIR) sharing of nanosafety data.

GenomeSpace Presentation

08 Feb 2016 | Presentations | Contributor(s): Michael Reich

GenomeSpace (http://www.genomespace.org) is a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes',...

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...

Hub Zero Status Update

21 Apr 2014 | Presentations | Contributor(s): Jayashree Kalpathy-Cramer, Vyshak Chandra

NCIP Hub, an environment to facilitate collaboration within the Quantitative Imaging Network

Image Analysis and Performance Metrics WG - DW and DCE MRI Update

21 Apr 2014 | Presentations | Contributor(s): Wei Huang, Tom Chenevert, Vyshak Chandra

IAPM-WG - DW and DCE MRI Update

Image Analysis and Performance Metrics WG - PET/CT Update

21 Apr 2014 | Presentations | Contributor(s): Jayashree Kalpathy-Cramer, Vyshak Chandra

IAPM-WG PET/CT Update

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

16 Sep 2014 | Publications | Contributor(s): Laura M Heiser, Nicholas J Wang, Carolyn L Talcott, Keith R Laderoute, Merrill Knapp, Yinghui Guan, Zhi Hu, Safiyyah Ziyad, Barbara L Weber, Sylvie Laquerre, Jeffrey R Jackson, Richard F Wooster, Wen Lin Kuo, Joe W Gray, Paul T Spellman

AbstractBackgroundCancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which...

Integrative Cancer Biology Program Datasets

26 Apr 2016 | Series | Contributor(s): Jonathan Bistline, Michael Reich

The NCI-ICBP promotes an integrative/systems approach to the study of cancer biology. The Program encourages scientists to study cancer as a complex biological system. Information gained from these studies are used to build reliable and testable predictive computation models of cancer processes...

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...

ITCR PI Meeting June 2014 Presentations

23 Jun 2014 | Series

Informatics Technology for Cancer Research (ITCR) Initiative held its Annual PI Meeting on June 12-13, 2014 in Rockville, MD. This series contains the presentations given at the meeting.

Jaqpot - An open-source web platform for creating, using, testing and sharing predictive models in nano-informatics

20 Jun 2019 | Presentations | Contributor(s): Haralambos Sarimveis

Nano WG June 20, 2019Computational models that predict physicochemical properties, biokinetics or adverse biological effects of Engineered Nanomaterials (ENMs) are becoming increasingly important to support risk assessment and safety-by-design. This is primarily due to cost-saving and...