Software Development to Enhance Echinobase

增强 Echinobase 的软件开发

• 批准号: 10715581
• 负责人: PETER D VIZE
• 金额: $ 17.52万
• 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/10715581
• 关键词: ATAC-seq; Architecture; Atlases; Award; Bioinformatics; Cells; Code; Collaborations; Communities; Computer software; Consultations; Consumption; Custom; Data; Data Set; Databases; Development; EchinoBase; Echinodermata; Educational workshop; Funding; Future; Gene Expression; Genes; Genome; Genomic Segment; Genomics; Genus Mentha; Goals; Grant; Head; High-Throughput Nucleotide Sequencing; Intuition; Link; Literature; Machine Learning; Maps; Methods; Orthologous Gene; Phase; Phenotype; Phylogenetic Analysis; Process; Regulatory Element; Research; Resources; Site; Specific qualifier value; Surveys; Synteny; System; Technology; Testing; Update; Variant; Visualization; Visualization software; Writing; XenBase; base; biomedical scientist; data access; data exchange; data modeling; data resource; data reuse; database query; database schema; design; empowerment; flexibility; genome browser; genome resource; genome-wide; improved; knowledgebase; member; middleware; migration; new technology; novel; paralogous gene; single cell technology; single-cell RNA sequencing; software development; symposium; technology development; tool; transcriptome sequencing; usability; web app; web interface; web portal

SUMMARY TECHNICAL DEVELOPMENT Software Development to Enhance Echinobase The Technical Development component describes software development for Echinobase. This includes code in the database, web applications, user and curator interfaces. New data types and new curation efforts require new systems, tools and software interfaces to be built. Importantly, interfaces must be designed to allow our community members to browse and interrogate the data via our web portal. We have recently added many new content types and features to Echinobase, including multi-species support, Gene, Literature and Community pages; and there are many additional types of content that will require support from the technical development team, including the GEO pipeline, single-cell omics, ortholog GO terms, tools to integrate paralog gene data and more. As many of the biologists generating and accessing these data are not bioinformaticians, we need to develop tools and interfaces that are intuitive and easy to use. An excellent example of how we plan to achieve this goal is the Xenbase GEO module that we will implement in Echinobase, that allows non-experts to view, interact with, and understand RNA-seq data through a simple, intuitive and interactive web interface. Over the next five years, we will proceed through numerous steps for each new type of data we aim to support: assessing data requirements, data modeling, middleware software development, testing and optimization of trial releases, developing curator, user and data browsing interfaces. Prioritization of projects is done in consultation with the echinoderm research community via annual surveys and workshops at conferences, input from our scientific advisory board and collaborators, and, in the future, in consultation with the Alliance of Genome Resources (AGR) workgroups and other external resources such as the NCBI and UCSC. Planned new projects include ATAC-seq data from GEO, paralog data from DIOPT, single-cell RNA-seq, support for genome wide CRE predictions, and computed expression phenotypes. Technical Development will also support our increased use of machine learning as applied to Echinobase literature and content curation. Aim 1. Support expanded and novel content. Aim 2. Generate custom content and support variants and single-cell datasets. Aim 3. Interface with external resources.

技术开发总结 增强 Echinobase 的软件开发 技术开发组件描述了 Echinobase 的软件开发。这包括代码 数据库、Web 应用程序、用户和管理者界面。新的数据类型和新的管理工作需要 将构建新的系统、工具和软件界面。重要的是，接口的设计必须允许我们 社区成员通过我们的门户网站浏览和查询数据。我们最近添加了许多新内容 Echinobase 的内容类型和功能，包括多物种支持、基因、文献和社区 页面；还有很多其他类型的内容需要技术开发的支持 团队，包括 GEO 管道、单细胞组学、直系同源 GO 术语、整合旁系同源基因数据的工具 等等。由于许多生成和访问这些数据的生物学家不是生物信息学家，我们需要 开发直观且易于使用的工具和界面。这是我们计划如何实施的一个很好的例子 实现这一目标的是我们将在 Echinobase 中实现的 Xenbase GEO 模块，它允许非专家 通过简单、直观和交互式的 Web 界面查看、交互和理解 RNA-seq 数据。 在接下来的五年中，我们将为我们旨在支持的每种新型数据采取众多步骤： 评估数据需求、数据建模、中间件软件开发、测试和优化 试用版，开发策展人、用户和数据浏览界面。项目的优先顺序是在 通过年度调查和会议研讨会与棘皮动物研究界进行磋商，提供意见 来自我们的科学顾问委员会和合作者，并在未来与联盟协商 基因组资源 (AGR) 工作组和其他外部资源，例如 NCBI 和 UCSC。计划 新项目包括来自 GEO 的 ATAC-seq 数据、来自 DIOPT 的旁系同源数据、单细胞 RNA-seq、支持 全基因组 CRE 预测和计算表达表型。技术开发也将 支持我们更多地使用机器学习应用于 Echinobase 文献和内容管理。 目标 1. 支持扩展和新颖的内容。 目标 2. 生成自定义内容并支持变体和单细胞数据集。 目标 3. 与外部资源的接口。