Informatics Technology for Cancer Research (ITCR) initiative [itcr]

 

Omics

The Bachelor (Collaborator) - A Statistician’s Tale Video

• Paul Marjoram, University of Southern California 

Short Videos to Promote Collaborative Opportunities in CIViC Video

• Obi Griffith, Washington University

A Statistical Framework to Systematically Characterize Cancer Driver Mutations in Noncoding Genomic Regions Video

• Eliezer Van Allen, Dana-Farber Cancer Institute

Personal Ad for UCSC Xena Video

• Mary Goldman, UC Santa Cruz Genomics Institute

Bioinformatics Technology to Characterize Tumor Infiltrating Immune Repertoires Video

• Li Song, Dana-Farber Cancer Institute

Open CRAVAT: Key Features and Opportunities for Collaboration Video

• Kym Pagel, Johns Hopkins University

Integration of Next-Generation Clustered Heat Maps and the GenePattern Notebook Environment Video

• Bradley Broom, MD Anderson Cancer Center

Computational Plugins for Next-Generation Clustered Heat Maps Video

• Bradley Broom, MD Anderson Cancer Center

OncoMX: A Knowledgebase of Cancer Biomarkers that Enables Searches of Unified Cancer Mutation and Expression Video

• Amanda Bell, The George Washington University

Cloud Accelerated Cancer Genomics with AnVIL and Bioconductor: Introduction Video

• Vincent Carey, Brigham and Women's Hospital

Bioconductor Meets GA4GH: Cloud-Scale Cancer Genomics with Standardized Workflow Processing Video

• Vincent Carey, Brigham and Women's Hospital

Harvesting 29000 cancer-related non-TCGA transcriptomes using Bioconductor and HDF Cloud Video

• Vincent Carey, Brigham and Women's Hospital

GenePattern Notebook 2020 Update Video

• Michael Reich, UC San Diego

cBio Portal Video

• Ethan Cerami, Dana-Farber Cancer Institute 

A Galaxy-Based Multi-Omic Informatics Hub for Cancer Researcher Video

• Tim Griffin, University of Minnesota

Globus Integration with MEV Video

• Brian Lawney, Harvard T.H. Chan School of Public Health

Leveraging WebMvE Backend for Single Cell RNASeq Analysis Video

• Yaoyu E. Wang, Harvard T.H. Chan School of Public Health

IGV Short Demonstration: Sharing Interactive Views with the IGV-Web Application Video

• Helga Thorvaldsdottir, Broad Institute

IGV Short Demonstration: Viewing evidence of alternative splicing in RNA-seq data with IGV's Sashimi Plot Video

• Helga Thorvaldsdottir, Broad Institute

Gene Set Enrichment Visualizations and Radial Plots Video

• Helga Thorvaldsdottir, Broad Institute

Gene Set Enrichment Analysis and Single Cell Data Video 

• Alex Wenzel, UC San Diego

TumorDecon Video

• Leili Shahriyari, University of Massachusetts Amherst

CNVpytor: A Python extension of CNVnator Video

• Alexej Abyzov, Mayo Clinic

Cistrome Explorer: Web-based Interactive Visualization Tool for Exploring Epigenomics Data with Associated Metadata Video

• Mark Keller, Harvard Medical School

AMARETTO-Hub: A Knowledge Graph Platform Embedding AMARETTO Tools for Multimodal and Multiscale Network BioMedicine Video

• Nathalie Pochet, Broad Institute

Toolkit for Annotating Mutations in the 3D Cancer Genome Video

• Kai Tan, University of Pennsylvania

TCPA: An Integrated Bioinformatics Resource for Cancer Functional Proteomics Data Video

• Han Liang, MD Anderson Cancer Center

 

Imaging

KiNet: A Novel Imaging Informatics Tool for Assessment of Ki67 Labeling Index Video

• Fuyong Xing, University of Colorado

Image Based Dosimetry from 90Y PET Using GATE: A Comparison Between Total-Body PET EXPLORER and Conventional PET Imaging Video  

• Gustavo Costa, UC Davis

XCIST: X-ray-based Cancer Imaging Simulation Toolkit Video

• Mingye Wu, GE Research

The TOPAS Tool for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical Research Video

• José Ramos-Méndez, UCSF

A Multi-resolution Model for Histopathology Image Classification and Localization Video

• Jiayun Li, UCLA

A Unified Machine Learning Package for Cancer Diagnosis Video

• Meredith (Wenjun) Wu, University of Washington

AI Assisted Pathology: A Tour of caMicroscope's Machine Learning Functionality Video

• Ryan Birmingham, Emory University

Tools to Analyze Morphology and Spatially Mapped Molecular Data: Quantitative Imaging for Pathology (QuIP) Software Platform Slides

• Tahsin Kurc, Stony Brook University

STAN-CT: Standardize and Normalize CT Images Video

• Md Selim, University of Kentucky

Federated Deep Learning Among Multiple Institutions for Automated Classification of Breast Density Video

• Ken Chang, Massachusetts General Hospital

The Federated Tumor Segmentation (FeTS) Platform: Intro Video

• Spyridon Bakas, University of Pennsylvania

Cancer Imaging Phenomics Toolkit (CaPTk): Deep Learning Based Segmentation and Radiomic Feature Extraction Video

Cancer Imaging Phenomics Toolkit (CaPTk): Interactive Machine Learning Based Segmentation Video

Cancer Imaging Phenomics Toolkit (CaPTk): Radiogenomics in Brain Tumors Video

Cancer Imaging Phenomics Toolkit (CaPTk): Breast Parenchymal Pattern Characterization - LIBRA Video

Cancer Imaging Phenomics Toolkit (CaPTk): Breast Radiomics Video

Cancer Imaging Phenomics Toolkit (CaPTk): Predicting Overall and Progression-Free Survival in Glioblastoma Video

Cancer Imaging Phenomics Toolkit (CaPTk): Predicting Glioblastoma Recurrence Location Video

Cancer Imaging Phenomics Toolkit (CaPTk): Distinguishing True- from Pseudo-Progression in Glioblastoma Video

• Spyridon Bakas, University of Pennsylvania

AI for Prostate: Detection and Grading of Prostate Cancer on Multiparametric MRI Video

• Karthik Sarma, UCLA

Quick Annotator: A Tool for Rapidly Annotating Digital Pathology Images Video

• Andrew Janowczyk, Case Western Reserve University

Prism - PathDB - Management of Pathology Images and FeatureMaps Slides

• Erich Bremer, Stony Brook University

PRISM Architecture Fundamentals Video

• Lawrence Tarbox, Univ. of Arkansas for Medical Sciences

PRISM Semantic Integration and Datascope Visual Exploration of Clinical Data in TCIA Lung Cancer Collections Video

• Jonathan Bona, University of Arkansas for Medical Sciences and Nan Li, Emory University

Preliminary MRI-Based Cellularity Predictions Indicate Abnormal Pathology in Brain Cancer Patients at Autopsy Video

• Samuel Bobholz, Medical College of Wisconsin

Multiplex Histology Registration Toolkit Video

• Michael Brehler, Medical College of Wisconsin

Developing Quality Ground Truth for Machine-Learning Algorithms in Pathology Video

• Mohamed Amgad,  Emory University

OHIF Viewer: An Extensible Open-Source Framework for Building Web-Based Imaging Applications to Support Cancer Research Video

• Gordon Harris, Harvard Medical School

Dataset Management in XNAT for Machine Learning Video

• Will Horton, Washington University in St. Louis

Model Training in XNAT with integrated NVIDIA Clara and TensorBoard Video

• Matt Kelsey, Washington University in St. Louis

Creating Millions of Synthetic DICOM Records for Testing Video

• Charlie Moore, Washington University in St. Louis

Pixel Anonymization on Upload using the XNAT Desktop App Video

• Stephen Moore, Washington University in St. Louis

Envisioning a DICOMweb Interface with XNAT Data Video

• David Maffitt, Washington University in St. Louis

PIIP: Intro to Sedeen - A Freely Available Pathology Viewer Video

• Dan Hosseinzadeh, Pathcore

 

Medical Informatics

EMERSE Import Tool Video

• David Hanauer, University of Michigan

The HemOnc Regimen Browser Video

• Jeremy Warner, Vanderbilt University

Genetic counseling at scale using EHR-integrated Chatbot technology Video

• Rick Bradshaw, University of Utah

An Expanded NLP Schema for Improved Cancer Risk Assessment of Family Health History (FHH) Video

• Keaton Morgan & Jianlin Shi, University of Utah

Identifying and Managing Patients Who Meet Evidence-Based Criteria for Genetic Evaluation of Familial Cancer Using the FHIR Data Standard Video

• Rick Bradshaw, University of Utah

Functional Precision Oncology for Cancer Treatment Selection Video

• Xiaomeng Huang, University of Utah

An Introduction to the Globus Research Data Management Service Video

• Ian Foster, University of Chicago

Globus: The Platform for Research Data Applications and Services Video

• Ian Foster, University of Chicago

MoldelHub.AI: Dissemination Platform for Deep Learning Models Video

• Ahmed Hosny, Dana Farber Cancer Institute 

Federated Analysis of Health and Genomics Data Video

• James Casaletto, UCSC

Patient-Derived Tumor Xenograft (PDX) Finder Video

• Nathalie Conte, EBI

Connecting Galaxy with the Cancer Research Data Commons Video

• Jeremy Goecks, Oregon Health & Science University

 

Networks

Graphic Rendering of Data in Your ITCR Web Tool Video

• Rudi Pillich, UC San Diego

Unifying and Comparing Multiple Kinase-substrate Prediction Networks for Reference Human Phosphoproteome Video

• Bingjie Xue, Benjamin Jordan, Saqib Rizvi and Kristen Naegle, University of Virginia

TransPRECISE: Personalized Network Modeling of the Pan-Cancer Patient and Cell Line Interactome Video

• Min Jin Ha, MD Anderson Cancer Center