Computational Support for All Echinobase Objectives

计算构成部分1：对所有Echinbase目标的计算支持 摘要 棘球数据库是唯一集中和精选的多个物种的基因组特征储存库 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，并 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 Xenbase的Xenopus模式生物体数据库。通过这种方式，Echinobase将收购 数据库，其中包含定制的Chado模式、基于Java的Web应用程序以及开发的各种其他工具 由Xenbase人员进行优化。具体地说，棘球蛋白将获得可搜索的基因表达数据库， 和高度自动化的管理管道。将定制自动化管道以加载和包含 棘皮动物特有的数据(即基因组、转录本、注释等)。该网站的前端将是 经过修改以投射独特的Echinobase用户界面，该界面支持Echinobase及其 用户首选项。因此，通过这项提议，Echinobase利用超过10年的时间和800万美元的 Xenbase的开发和专业知识。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。这种创新且节省成本的方法支持 Echinobase的扩展功能(即增加了基因表达数据库)以及 更广泛的数据库合并倡议。将为部署以下项目提供计算支持 BioTapestry，一款基因调控网络建模和查看软件，建议与 棘球绦虫。该组件还将为数据、管理和软件创新提供关键支持 这个应用程序的其他组件；它是整个棘球虫数据库的主干。

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.