"Show me the data!" Practical solutions to interactive visual analysis for big data.
18 Sep 2015 | Contributor(s): Samuel Payne
Nano WG September 10, 2015.Intuitive data visualization is critical for biomedical data analysis; especially essential is the ability for non-computational scientists to productively browse the data and apply their domain knowledge. We present Active Data Biology, a web-based visual...
A Semantic Web-based Quality Assurance Tool for Cancer Study Common Data Elements
16 Jun 2015 | Presentations | Contributor(s): Guoqian Jiang
A poster presentation from the caCDE-QA project (PI: Jiang)
Accelerating Nanotech Innovations Through a Safer-By-Design Approach, Safer Nanomaterials School
14 May 2019 | Presentations | Contributor(s): Philippe Sabatier
Nano WG May 9, 2019European Scientific Institute (ESI) Safer Nanomaterials School Introduction.
Activities to Promote Technology Research Collaborations (APTRC) PA-17-143 Pre-Application Webinar
24 Feb 2017 | Presentations | Contributor(s): Juli Klemm, Tony Dickherber
Pre-application seminar held February 24, 2017 for FOA PA-17-143
Advanced Development of TIES - A Clinical Text Search Engine
18 Feb 2014 | Presentations | Contributor(s): Rebecca Crowley
Archived human tissues are an essential resource for translational research. Formalin-fixed, paraffin-embedded (FFPE) tissues from cancer patients are used in a wide range of assays, including RT-PCR, SNP profiling, multiplex biomarkers, imaging biomarkers, targeted exome, whole exome, and whole...
An Extensible and Scalable Knowledge System Architecture for Cancer Research
06 May 2016 | Presentations | Contributor(s): Daniel Crichton
ITCR May 2016 PI meeting presentation on development of an advanced knowledge system to capture, share and support reproducible analysis from the biomarker data results.
Analysis, integration and visualization of DNA methylation sequencing data
07 Nov 2014 | Presentations | Contributor(s): Maureen Sartor
Integrative epigenomic/genomic profiling and biomarker discovery of HPV+ and HPV- squamous cancers.
Biomedical Evidence Graph
03 Oct 2014 | Presentations | Contributor(s): Josh Stuart
Brain Cancer Imaging Analytics
02 Oct 2015 | Presentations | Contributor(s): Christos Davatzikos
The transition of oncologic imaging from its “industrial era” to it is “information era” demands analytical methods that 1) extract information from this data that is clinically and biologically relevant; 2) integrate imaging, clinical, and genomic data via rigorous...
caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine
13 Dec 2013 | Publications | Contributor(s): Sharon Gaheen, George W Hinkal, Stephanie A Morris, Michal Lijowski, Mervi Heiskanen, Juli Klemm
The use of nanotechnology in biomedicine involves the engineering of nanomaterials to act as therapeutic carriers, targeting agents and diagnostic imaging devices. The application of nanotechnology in cancer aims to transform early detection, targeted therapeutics and cancer prevention and...
Cloud Supercomputer Aided Diagnostic Imaging Decision Support System
18 Jun 2014 | Presentations | Contributor(s): Hiro Yoshida
ITCR PI meeting presentation on project status.
CRAVAT - Cancer-Related Analysis of Variants Toolkit
23 Jun 2015 | External Applications | Contributor(s): Rachel Karchin, Michael C Ryan
cravat is a bioinformatics pipeline : ; that performs high-throughput cancer-related analysis of variants. it : ; utilizes three applications: CHASM (Cancer-Specific Analysis of Somatic Mutations), VEST and SVN-Get. More information on these tools is available at CHASM Software.Release...
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...
Development of natural language processing tools for nanoparticle design
05 Mar 2019 | Presentations | Contributor(s): Nastassja Lewinski
Nano WG February 28, 2019: In this presentation, an introduction to the application of natural language processing techniques to nanotechnology data will be discussed. Natural language processing tools can aid in the automatic categorization, extraction, and analysis of data from...
Development of Targeted Nanomedicines via Machine Learning Processes
05 Mar 2019 | Presentations | Contributor(s): Daniel Heller
Nano WG February 21, 2019Description: We are using data science to facilitate the development of nanoparticle drugs incorporating kinase inhibitors with diverse chemical structures. Doing this work inspired us to bring together the nanoinformatics community...
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...
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',...
Informatics to enable Routine Personalized Cancer Therapy (IPCT)
18 Feb 2014 | Presentations | Contributor(s): Elmer V. Bernstam, Funda Meric-Bernstam
Informatics Tools for High-throughput Analysis of Cancer Mutations
15 Jan 2014 | Presentations | Contributor(s): Michael C Ryan, Rachel Karchin
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...