Bioinformatics/IT and Data Sharing Working Group Update

21 Apr 2014 | Presentations | Contributor(s): Brad Erickson, Tom Casavant, John Freymann, Vyshak Chandra

Bioinformatics/IT and Data Sharing Working Group Update

BioIT Call To Action

28 Apr 2022 | Publications | Contributor(s): Anil Srivastava, Nicholas Siebenlist, Jane J Yu, Bishen Singh

Call to action to join cancer patient digital twin consortium in advance of BioIT-World Conference, held May 3rd-5th. 

Biospecimen and Clinical Trials Educational Videos in Asian Languages

24 Nov 2015 | Teaching Materials | Contributor(s): Julie Dang

Culturally appropriate, ethnic specific, community tested biospecimen and clinical trials educational videos in multiple Asian American languages (Chinese, English, Hmong, Ilokano, Korean, Tagalog, and Vietnamese). 

Biospecimen NCI PPT

24 Nov 2015 | Teaching Materials | Contributor(s): NCI

This NCI presentation was originally used at the UNM Cancer Center by the NON/CHE (Maria Otero).

Breast Cancer Crossword

20 Nov 2015 | Teaching Materials | Contributor(s): Katelyn Schifano

This crossword is designed for use in social media as well as patient waiting areas.

BRIDG 4.0 HTML.zip

08 Dec 2015 | Downloads | Contributor(s): Wendy Nan Ver Hoef, Smita Hastak, Lloyd Mckenzie, Julie Evans, Boris Brodsky

Download this file to save and install a local copy of the HLTML version of BRIDG 4.0. The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 BRIDG Work Group, the US...

BRIDG Imaging Project Description

25 Nov 2015 | Presentations | Contributor(s): Smita Hastak, Wendy Verhoef

11/25/2015 meeting slides

Building Online Scientific Communities via NCIP Hub

17 Nov 2014 | Teaching Materials | Contributor(s): Ishwar Chandramouliswaran

Overview of how NCIP Hub can be used to build online scientific communities.

Building the Knowledgebase of Biology using Citizen Science

12 Jun 2015 | Presentations | Contributor(s): Andrew Su

Andrew Su discusses Mark2Cure and how to build a knowledgebase of biology using citizen science.

caCDE-QA: A quality assurance platform for cancer study common data elements

26 Mar 2015 | Presentations | Contributor(s): Guoqian Jiang

This is a presentation about an overview of a NCI ITCR U01 project - caCDE-QA: A quality assurance platform for cancer study common data elements (PI, Guoqian Jiang, Mayo Clinic). The goal of the project is to design, develop and evaluate an integrative platform known as caCDE-QA that implements...

CAFCW 104 Deep kernel Learning for Information Extraction from Cancer Pathology Reports

05 Dec 2019 | Presentations | Contributor(s): Devanshu Agrawal, Abhishek Dubey, Georgia Tourassi, Jacob Hinkle

Cancer pathology reports comprise a rich source of data for surveilling cancer incidents and tracking cancer trends across the United States. Cancer registries manually extract key pieces of information from these reports including tumor site, histology, laterality, behavior, grade, and...

CAFCW 104 Deep Kernel Learning for Information Extraction from Cancer Pathology Reports

09 Dec 2019 | Presentations | Contributor(s): Devanshu Agrawal, Abhishek Dubey, Georgia Tourassi, Jacob Hinkle

Cancer pathology reports comprise a rich source of data for surveilling cancer incidents and tracking cancer trends across the United States. Cancer registries manually extract key pieces of information from these reports including tumor site, histology, laterality, behavior, grade, and...

CAFCW 105 Acceleration of Hyperparameter Optimization via Task Parallelism for Information Extraction from Cancer Pathology Reports

09 Dec 2019 | Presentations | Contributor(s): John Gounley, Hong-Jun Yoon

Recent advances in high-performance computing systems for artificial intelligence enable large-scale training of information extraction models from free-form natural language texts. The development of these models is essential to the cancer surveillance research and automation. In this study, we...

CAFCW 113 Digital Twins for Predictive Cancer Care: an HPC-Enabled Community Initiative

09 Dec 2019 | Presentations | Contributor(s): Emily Greenspan, Carolyn Lauzon, Amy Gryshuk, Jonathan Ozik, Nicholson Collier, Tanveer Syeda-Mahmood, Ilya Shmulevich, Tina Hernandez-Boussard, Paul Macklin

Cancer is a complex multiscale dynamical systems problem with interactions between the tumor and host at the molecular, cellular, tissue, and organism levels. Moreover, treatment occurs within a larger dynamical system that couples clinical care teams, hospital systems, industry, and government...

CAFCW 120 Integrating High-Performance Simulations and Learning toward Improved Cancer Therapy

09 Dec 2019 | Presentations | Contributor(s): Austin Clyde, Dave Wright, Shantenu Jha

We develop a novel deep learning workflow to effectively combine expensive but accurate molecular dynamics (MD) based BFE calculations with fast machine learning models to predict the affinity of compounds. In this approach, candidates are sampled from a large billion-compound synthetically...

CAFCW 122 Fusion of Structure Based Deep Learning to Accelerate Molecular Docking Predictions

09 Dec 2019 | Presentations | Contributor(s): Derek Jones

Modeling interactions with biological targets is a necessary step to begin reasoning about the therapeutic potential of a novel molecule in the drug discovery process. Molecular docking aids drug discovery researchers by searching over potential binding ‘poses’ of a drug molecule,...

CAFCW109 Semi-Supervised Method for Countering Batch Effect

06 Dec 2019 | Presentations | Contributor(s): Stewart He

Predictive modeling of patient tumor growth response to drug treatment is severely limited by a lack of experimental data for training. Combining experimental data from several studies is an attractive approach, but presents two problems: batch effects and limited data for individual drugs and...

CAFCW115 Massively Parallel Large-Scale Multi-Model Simulation of Tumor Development including Treatments

19 Dec 2019 | Presentations | Contributor(s): Marco Berghoff, Jakob Rosenbauer, Alexander Schug

The temporal and spatial resolution in the microscopy of tissues has increased significantly within the last years, yielding new insights into the dynamics of tissue development and the role of the single-cell within it. A thorough theoretical description of the connection of single-cell...