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：所有Echinobase目标的计算支持 总结 Echinobase是唯一一个集中和策划的多个物种的基因组特征库， 棘皮动物访问Echinobase资源的主要模式是通过网络信息系统， 将存储在注释数据库中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， 通过定期升级和维护所有系统，确保该系统保持最佳性能 软件和硬件。该组件通过从克隆实现系统构建来满足这些需求 非洲爪蟾模式生物数据库。通过这种方式，Echinobase将获得 数据库与自定义Chado模式，基于Java的Web应用程序，以及各种其他开发工具， 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， 和高度自动化的策展管道。自动化管道将被定制为装载和容纳 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 修改后的项目独特的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多年的时间和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 其成本仅为单独提供更新的一小部分。这种创新和节省成本的方法支持 扩展Echinobase的功能（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 BioTapestry是一个基因调控网络建模和查看软件，建议与 海胆该组件还将为以下方面的数据、策展和软件创新提供关键支持： 这个应用程序的其他组件;它是整个Echinobase的支柱。