Computational Support for All Echinobase Objectives

对所有 Echinobase 目标的计算支持

• 批准号: 10241293
• 负责人: PETER D VIZE
• 金额: $ 15.43万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-20 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10241293
• 关键词: Address; Binding Sites; Biological Models; Biological Sciences; Communities; Computer software; Cost Savings; Custom; Data; Data Set; Databases; Development; EchinoBase; Echinodermata; Elements; Ensure; Environment; Future; Gene Expression; Genes; Genome; Genomics; Goals; Human Resources; Informatics; Information Systems; Infrastructure; Internet; Java; Literature; Maintenance; Online Systems; Ontology; Output; Paper; Performance; Privatization; Regulator Genes; Research; Resources; Secure; System; Update; Vertebral column; XenBase; base; cost; data curation; gene expression database; genome annotation; genome resource; innovation; interest; member; network models; preference; repository; system architecture; technology development; tool; transcription factor; transcriptome; virtual machine; web app; web page; web site; web-accessible

Computational Component 1: Computational Support for all Echinobase Objectives SUMMARY Echinobase is the only centralized and curated repository of genomic features for multiple species of echinoderms. The primary mode of access to Echinobase resources is through a web information system that displays content stored in annotation databases as useful and informative web pages and applications. This requires maintaining data and applications in a secure, high performance, web-accessible environment and ensuring that this system remains at peak performance through regular upgrading and maintenance of all software and hardware. This component addresses these needs by implementing a system build from a clone of Xenbase, the Xenopus model organism database. Through this approach Echinobase will acquire the database with a customized Chado schema, a java based web app, and various other tools developed and optimized by Xenbase personnel. In particular Echinobase will acquire a searchable gene expression database, and highly automated curation pipelines. Automated pipelines will be customized to load and contain echinoderm-specific data (i.e. genomes, transcriptomes, annotations, etc). The website frontend will be modified to project a unique Echinobase user interface that supports the unique features of Echinobase and its users preferences. Thus, through this proposal, Echinobase leverages more than 10 years and $8 million of Xenbase development and expertise. This provides an extensive improvement in functionality for Echinobase at a fraction of the cost of providing updates in isolation. This innovative and cost saving approach supports both expanded functionalities of Echinobase (i.e. the addition of a gene expression database) as well as broader initiatives of database coalescence. Computational support will be provided for the deployment of BioTapestry, a gene regulatory network modeling and viewing software addition proposed to integrate with Echinobase. This component will also provide critical support the data, curation, and software innovations from the other components of this application; it is the backbone of the entirety of Echinobase.

计算组件 1：对所有 Echinobase 目标的计算支持 概括 Echinobase 是唯一一个集中且精心策划的多个物种基因组特征存储库 棘皮动物。访问 Echinobase 资源的主要方式是通过网络信息系统， 将注释数据库中存储的内容显示为有用且信息丰富的网页和应用程序。这 需要在安全、高性能、可通过 Web 访问的环境中维护数据和应用程序，并且 通过定期升级和维护所有系统，确保该系统保持最佳性能 软硬件。该组件通过从克隆实现系统构建来满足这些需求 Xenbase，非洲爪蟾模式生物数据库。通过这种方式，Echinobase 将收购 具有定制 Chado 模式的数据库、基于 Java 的 Web 应用程序以及开发和使用的各种其他工具 由Xenbase人员优化。特别是 Echinobase 将获得一个可搜索的基因表达数据库， 和高度自动化的管理管道。自动化管道将被定制来装载和容纳 棘皮动物特异性数据（即基因组、转录组、注释等）。网站前端将是 修改为项目独特的 Echinobase 用户界面，支持 Echinobase 的独特功能及其 用户偏好。因此，通过这项提案，Echinobase 利用了 10 多年的资金和 800 万美元的资金 Xenbase 开发和专业知识。这为 Echinobase 的功能提供了广泛的改进 其成本只是单独提供更新的一小部分。这种创新且节省成本的方法支持 Echinobase 的扩展功能（即添加基因表达数据库）以及 更广泛的数据库合并举措。将为部署提供计算支持 BioTapestry，一种基因调控网络建模和查看软件，建议与 刺碱。该组件还将为数据、管理和软件创新提供关键支持 该应用程序的其他组件；它是整个 Echinobase 的支柱。