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