Human Tumor Atlas Network: Data Coordinating Center Supplement

人类肿瘤图谱网络：数据协调中心补充

• 批准号: 10206514
• 负责人: Ethan Cerami
• 金额: $ 92.64万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-30 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10206514
• 关键词: Acute; Address; Atlases; Bioinformatics; Biopsy; Client; Code; Collaborations; Complex; Computational algorithm; Computer software; Coupled; Custom; Data; Data Analyses; Data Collection; Data Coordinating Center; Databases; Development; Diagnosis; European; General Population; Generations; Goals; Human; Image; Imaging Device; Informatics; Infrastructure; Institutes; Lead; Malignant Neoplasms; Manuscripts; Methods; Modeling; Molecular; Operative Surgical Procedures; Output; Pathologist; Performance; Reporting; Side; Slide; Software Tools; Specimen; System; Technology; Testing; Tissue imaging; Tissues; Vertebral column; Visualization; base; cancer imaging; cellular imaging; cloud based; computing resources; data dissemination; data management; data resource; data visualization; imaging Segmentation; imaging informatics; improved; machine learning algorithm; multiplexed imaging; programs; relational database; single cell sequencing; software development; supervised learning; tumor

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.

该提案是与HTAN数据协调中心DCC的合作， 图像数据项目旨在开发和部署存储所需的技术， 由多个HTAN中心收集的细胞和组织图像的分布和基本分析。 多重组织图像是几乎所有中心的重要数据类型， HTAN（在收集数据的中心数量上仅次于单细胞测序数据）。 然而，该软件需要可视化、分析、管理和共享多路复用图像 组织和肿瘤发育不全。SARDANA图像的最初可用性 强调了HTAN（包括DCC）在部署基础设施方面面临的挑战， 分发大型和复杂的图像。因此，我们提出了一个为期两年的HTAN图像数据 由DCC和HMS PCA领导的IDP项目侧重于快速开发和部署 用于图像管理和分析的图像信息系统和计算资源。 我们的目标是不迟于2020年夏季部署第一代系统， 然后稳步完善该系统，使其成为跨职能HTAN的骨干 地图集作为一个必要的问题，我们将开始与信息系统和软件， 无论是今天可用的还是处于相对先进的发展状态。但是，我们希望 在整个IDP中评估这些选择，并在必要时改变路线， 潜在的上级方法。我们还将支持中心的多样化需求和形式 使用不同的数据收集方法。目标1将侧重于部署和渐进 基于OMERO的图像管理云数据库的改进 标准以及用于访问原始数据并行系统。Aim 2将开发和部署 HTAN图像数据的可视化软件。IDP将使用现有的 MCWG和DAWG的监督和报告机制，以及所有中心将被邀请 参加在国内流离失所者方案内，皇家海军警察事务局将主要负责初步部署 图像信息学软件。DCC和HMS将共同进行软件开发， 代码强化，DCC将在用户协助和软件部署方面发挥主导作用， 尤其是在第二年。