Justin Guinney, Ph.D. - US grants

PROJECT SUMMARY Over the past decade, the CTSAs have made incredible progress in developing informatics tools and services to support institutional or hub-centric translational research. However, robust collaboration between the hubs is required to realize the full potential of the CTSA network, a living ecosystem of collaboration and sharing. We have brought together pioneers of open science, clinical and biomedical informatics, health science libraries, and the NCATS Translator initiative to propose the creation of a National Center for Digital Health Innovation to coalesce the CTSA informatics community together with the open science community to catalyze the next steps in the evolution of biomedical informatics. We will create an open governance model that includes all who would like to participate and collaboratively forge the next steps. We will embrace an ?idea to implementation? model (I2I), supporting the creation of collaboratively developed sustainable infrastructure. We will do this via the axes of open data, open software, open resources, and through two integrated thematic areas of urgent need: rare disease and human health across the lifespan. Underpinning these efforts are innovative models for evaluation, training, and the creation of community challenges as mechanisms to stimulate new and impactful tools and methods. We will leverage the power of an open and team science approach to demonstrate new research opportunities. Our leadership include Oregon Health Sciences University, Johns Hopkins University, the University of Washington, Washington University in St. Louis, Northwestern University, Sage BioNetworks, the Jackson Laboratory and the Scripps Research Institute. We have collaborators from all areas of translational informatics including health record vendors, clinical research networks and leaders in open software and open data. Together our efforts will catalyze the next stage in the evolution of the national informatics infrastructure for clinical and translational research.

PROJECT SUMMARY Over the past decade, the CTSAs have made incredible progress in developing informatics tools and services to support institutional or hub-centric translational research. However, robust collaboration between the hubs is required to realize the full potential of the CTSA network, a living ecosystem of collaboration and sharing. We have brought together pioneers of open science, clinical and biomedical informatics, health science libraries, and the NCATS Translator initiative to propose the creation of a National Center for Digital Health Innovation to coalesce the CTSA informatics community together with the open science community to catalyze the next steps in the evolution of biomedical informatics. We will create an open governance model that includes all who would like to participate and collaboratively forge the next steps. We will embrace an ?idea to implementation? model (I2I), supporting the creation of collaboratively developed sustainable infrastructure. We will do this via the axes of open data, open software, open resources, and through two integrated thematic areas of urgent need: rare disease and human health across the lifespan. Underpinning these efforts are innovative models for evaluation, training, and the creation of community challenges as mechanisms to stimulate new and impactful tools and methods. We will leverage the power of an open and team science approach to demonstrate new research opportunities. Our leadership include Oregon Health Sciences University, Johns Hopkins University, the University of Washington, Washington University in St. Louis, Northwestern University, Sage BioNetworks, the Jackson Laboratory and the Scripps Research Institute. We have collaborators from all areas of translational informatics including health record vendors, clinical research networks and leaders in open software and open data. Together our efforts will catalyze the next stage in the evolution of the national informatics infrastructure for clinical and translational research.

PROJECT SUMMARY Over the past decade, the CTSAs have made incredible progress in developing informatics tools and services to support institutional or hub-centric translational research. However, robust collaboration between the hubs is required to realize the full potential of the CTSA network, a living ecosystem of collaboration and sharing. We have brought together pioneers of open science, clinical and biomedical informatics, health science libraries, and the NCATS Translator initiative to propose the creation of a National Center for Digital Health Innovation to coalesce the CTSA informatics community together with the open science community to catalyze the next steps in the evolution of biomedical informatics. We will create an open governance model that includes all who would like to participate and collaboratively forge the next steps. We will embrace an `idea to implementation' model (I2I), supporting the creation of collaboratively developed sustainable infrastructure. We will do this via the axes of open data, open software, open resources, and through two integrated thematic areas of urgent need: rare disease and human health across the lifespan. Underpinning these efforts are innovative models for evaluation, training, and the creation of community challenges as mechanisms to stimulate new and impactful tools and methods. We will leverage the power of an open and team science approach to demonstrate new research opportunities. Our leadership include Oregon Health Sciences University, Johns Hopkins University, the University of Washington, Washington University in St. Louis, Northwestern University, Sage BioNetworks, the Jackson Laboratory and the Scripps Research Institute. We have collaborators from all areas of translational informatics including health record vendors, clinical research networks and leaders in open software and open data. Together our efforts will catalyze the next stage in the evolution of the national informatics infrastructure for clinical and translational research.

This proposal is a collaboration with the HTAN Data Coordination Center DCC and describes an Image Data Project aimed at developing and deploying the technology needed for storage, distribution and basic analysis of cell and tissue images collected by multiple HTAN Centers. Multiplexed tissue images are an important type of data for nearly all of the centers contributing to the HTAN (second only to single cell sequencing data in number of centers collecting data). However, the software needed to visualize, analyze, manage, and share multiplexed images of tissues and tumors is underdeveloped. The initial availability of SARDANA images has highlighted the challenges faced by HTAN, including the DCC, in deploying an infrastructure for distributing large and complex images. We therefore propose a two-year HTAN Image Data Project (IDP) led by the DCC and HMS PCA focused on the rapid development and deployment of image informatic systems and computational resources for image management and analysis. Our goal is to put in place a functional first-generation system no later than summer 2020 and to then steadily refine the system so that it becomes the backbone of cross-functional HTAN atlases. As a matter of necessity, we will start with informatic systems and software that are either available today or in a relatively advanced state of development. However, we expect to evaluate these choices throughout the IDP and change course as necessary to incorporate potentially superior approaches. We will also support the diverse needs and formats of centers using different data collection methods. Aim 1 will focus on the deployment and progressive improvement of a cloud-based database for image management based on the OMERO standard as well as a parallel system for access to primary data. Aim 2 will develop and deploy software for visualizing HTAN image data by the general public. The IDP will use the existing MCWG and DAWG mechanisms for oversight and reporting, and all centers will be invited to participate. Within IDP, the HMS PCA will take primary responsibility for initial deployment of image informatics software. The DCC and HMS will jointly undertake software development and code hardening, and the DCC will take the lead in user assistance and software deployment, particularly in year two.