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.

技术发展综述 增强棘球数据库的软件开发 技术开发组件描述了Echinobase的软件开发。这包括 数据库、Web应用程序、用户和馆长界面。新的数据类型和新的管理工作需要 将建立新的系统、工具和软件接口。重要的是，接口必须设计成允许我们的 社区成员可以通过我们的门户网站浏览和询问数据。我们最近增加了许多新的 棘球数据库的内容类型和特征，包括多物种支持、基因、文献和社区 页面；还有许多其他类型的内容需要技术开发人员的支持 团队，包括GEO管道，单细胞组学，正向同源围棋术语，整合Paralog基因数据的工具 还有更多。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、易用的工具和界面。一个很好的例子，说明了我们计划如何 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、直观和交互的Web界面查看、交互和理解RNA-seq数据。 在接下来的五年里，我们将针对我们要支持的每一种新数据类型执行多个步骤： 评估数据需求、数据建模、中间件软件开发、测试和优化 试行发布，开发馆长、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讲习班与棘皮动物研究界进行协商，提供投入 来自我们的科学顾问委员会和合作者，并在未来与 基因组资源(AGR)工作组和其他外部资源，如NCBI和UCSC。计划中的 新项目包括来自GEO的ATAC-SEQ数据，来自DIOPT的Paralog数据，单细胞RNA-SEQ，支持 全基因组Cre预测和计算的表达表型。技术开发还将 支持我们更多地使用机器学习，将其应用于棘库文献和内容管理。 目标1.支持扩展和新颖的内容。 目标2.生成定制内容并支持变体和单元格数据集。 目标3.与外部资源对接。