Xenbase - Tech Development

构成部分：技术开发 项目总结/摘要 技术开发组件描述Xenbase的软件开发。这 包括数据库中的代码、Web应用程序、用户和管理员界面。新的数据类型和 新的管理工作需要建立新的系统、工具和软件接口。重要的是， 界面的设计必须允许我们的社区成员浏览和查询数据 通过我们的门户网站。我们最近向Xenbase添加了许多新的内容类型，包括RNA- 来自GEO的seq和ChIP-seq数据，以及解剖学和表达表型; 许多其他类型的内容需要技术开发团队的支持， 包括单细胞组学，组学可视化的聚类工具，可视化人类的工具， 疾病变体和爪蟾表型。正如许多生物学家产生和访问 这些数据不是生物信息学家，我们需要开发直观的工具和界面， 和易于使用的.我们最近发布的GEO就是一个很好的例子 模块，允许非专家查看，互动，并通过理解RNA-seq数据， 简单、直观和交互式的Web界面。在未来五年，我们将继续 我们旨在支持的每种新数据类型的许多步骤：评估数据要求， 数据建模、中间件软件开发、测试和优化试用版， 开发管理员、用户和数据浏览界面。项目的优先次序是在 通过年度调查和研讨会与非洲爪蟾研究界进行磋商， 会议，我们的外部咨询委员会和合作者的投入，并在未来， 与基因组资源联盟（AGR）工作组进行磋商。计划新开工项目 包括来自GEO ATAC-seq数据、来自DIOPT的orthology数据、单细胞RNA-seq、对 人类疾病变异和单细胞组学。技术开发也将支持我们的 增加机器学习在爪蟾文献管理中的应用。 目标1：支持扩展和新颖的内容。 目标2：生成自定义内容，并通过外部 资源 目标3：与外部资源的接口。

Component: TECHNOLOGY DEVELOPMENT PROJECT SUMMARY/ABSTRACT The Technology Development component describes software development for Xenbase. 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 to Xenbase, including RNA- seq and ChIP-seq data from GEO, and anatomical and expression phenotypes; and there are many additional types of content that will require support from technology development team, including single-cell omics, clustering tools for omics visualization, tolls to visualize human disease variants and Xenopus phenotypes. 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 achieved this is our recently released GEO module 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 to type of data we aim to support: assessing data requirements, data modeling, middleware software development, testing and optimization of trial releases, develop curator, user and data browsing interfaces. Prioritization of projects is done in consultation with the Xenopus research community via annual surveys and workshops at conferences, input from our external advisory board and collaborators, and, in the future, in consultation with the Alliance of Genome Resources (AGR) workgroups. Planned new projects include ATAC-seq data from GEO, orthology data from DIOPT, single-cell RNA-seq, support for human disease variants and single-cell omics. Technology Development will also support our increased use of machine learning as applied to Xenopus literature curation. Aim 1: Support expanded and novel content. Aim 2: Generate custom content and support variants and single-cell datasets via external resources. Aim 3: Interface with external resources.