Computational Support for All Echinobase Objectives

对所有 Echinobase 目标的计算支持

• 批准号: 10715582
• 负责人: PETER D VIZE
• 金额: $ 15.79万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-22 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10715582
• 关键词: Award; Code; Communities; Complex; Computer software; Custom; Data; Databases; Development; EchinoBase; Echinodermata; Ensure; Environment; FAIR principles; Future; Genes; Genome; Genomics; Goals; Hybrids; Infrastructure; Licensing; Monitor; Performance; Privatization; Process; Production; Publications; Reporting; Research Personnel; Resources; Risk; Running; Secure; Services; System; Testing; Time; Update; Work; code development; computerized data processing; computing resources; data exchange; data management; diverse data; improved; knowledgebase; migration; open source; open source tool; response; time use; tool; tool development; virtual machine; web app; web interface

SUMMARY COMPUTATIONAL 1 Computational Support for all Echinobase Objectives The goal of the Computation component is to keep Echinobase operational, reliable, and responsive, to maintain and upgrade the hardware, cloud, infrastructure, software and systems necessary for peak performance and to develop and support the proposed improvements described in other sections of this application. Knowledgebases like Echinobase must integrate and process a diverse array of data and provide users with tools and interfaces to query and explore its content. These are all computational processes. In addition, Echinobase must interface with external databases and resources (NCBI, the AGR, publishers) to synchronize content and to provide annotated echinoderm data. Although invisible to the user, there is a considerable amount of computing that occurs behind the scenes every time a researcher uses Echinobase. Echinobase is a complex computing environment consisting of multiple, separate databases, many different software applications, user and curator web interfaces, and many automated data exchange pipelines. To ensure stability and enhance performance, tool sets are isolated on their own virtual machines (VMs) - we currently run ~10 VMs in our private cloud - and we constantly monitor, test, maintain, and fix bugs to keep it all running smoothly. Each time new software is implemented, we test it on isolated VMs, then optimize and integrate it with existing systems. Many of these systems, including the database and the web application server, will be migrated to new systems in the new cycle, along with a move from private cloud to the public cloud. All of this activity is contained within the Computation component and is paramount to achieving our overall project goals. In this component, we describe the computing work needed to maintain current functionality, generate custom content and the resources necessary to implement expansions and improvements over the next award cycle. Aim 1. Migrate software stack to open source systems and implement core features on the commercial cloud Aim 2. Maintain and expand computation of Echinobase content Aim 3. Manage and monitor networking and systems

总结计算 1 对所有 Echinobase 目标的计算支持 计算组件的目标是保持 Echinobase 的可运行性、可靠性和响应能力，以 维护和升级高峰所需的硬件、云、基础设施、软件和系统 性能，并开发和支持本节其他部分中描述的拟议改进 应用。像 Echinobase 这样的知识库必须集成和处理各种数据并提供 用户可以使用工具和界面来查询和探索其内容。这些都是计算过程。在 此外，Echinobase 必须与外部数据库和资源（NCBI、AGR、出版商）连接，以 同步内容并提供带注释的棘皮动物数据。虽然用户看不到，但有一个 每次研究人员使用 Echinobase 时，都会在幕后进行大量计算。 Echinobase 是一个复杂的计算环境，由多个独立的数据库、许多不同的数据库组成 软件应用程序、用户和管理者 Web 界面以及许多自动化数据交换管道。到 确保稳定性并增强性能，工具集隔离在自己的虚拟机 (VM) 上 - 我们 目前在我们的私有云中运行约 10 个虚拟机 - 我们不断监控、测试、维护和修复错误以保留所有虚拟机 运行顺利。每次实施新软件时，我们都会在隔离的虚拟机上进行测试，然后进行优化和 将其与现有系统集成。其中许多系统，包括数据库和 Web 应用程序 服务器，将在新周期迁移到新系统，同时从私有云迁移到公共云 云。所有这些活动都包含在计算组件中，对于实现我们的目标至关重要 项目总体目标。在此组件中，我们描述了维持当前状态所需的计算工作 功能，生成自定义内容和实现扩展所需的资源 下一个奖励周期的改进。 目标1.将软件堆栈迁移到开源系统并在商业云上实现核心功能 目标 2. 维护和扩展 Echinobase 内容的计算 目标 3. 管理和监控网络和系统