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

摘要计算1 所有Echinobase目标的计算支持 计算组件的目的是保持echinobase的操作，可靠和响应迅速， 维护和升级高峰的硬件，云，基础架构，软件和系统 绩效并发展和支持其他部分所述的提议改进 应用。诸如Echinobase之类的知识库必须集成和处理各种数据并提供 用户使用工具和接口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，Publishers）接口到 同步内容并提供带注释的棘皮动物数据。尽管用户看不见，但有一个 每当研究人员使用echinobase时，幕后都会发生大量计算。 echinobase是一个复杂的计算环境，由多个单独的数据库组成，许多不同 软件应用程序，用户和策展人Web界面以及许多自动数据交换管道。到 确保稳定性并提高性能，在自己的虚拟机（VM）上隔离工具集 - 我们 目前在我们的私有云中运行〜10 vm-我们不断监视，测试，维护和修复错误以保持所有内容 运行顺利。每次实施新软件时，我们都会在孤立的VM上进行测试，然后优化和 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 服务器将在新周期中迁移到新系统，以及从私有云到公众的转变 云。所有这些活动都包含在计算组件中，对于实现我们的 总体项目目标。在此组件中，我们描述了维护当前所需的计算工作 功能，生成自定义内容以及实施扩展所需的资源和 在下一个奖励周期中的改进。 目标1。迁移软件堆栈以开源系统并在商业云上实现核心功能 目标2。维护和扩展棘皮动物酶含量的计算 AIM 3。管理和监视网络和系统