Software Development to Enhance Echinobase
增强 Echinobase 的软件开发
基本信息
- 批准号:10715581
- 负责人:
- 金额:$ 17.52万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 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:
- 关键词:ATAC-seqArchitectureAtlasesAwardBioinformaticsCellsCodeCollaborationsCommunitiesComputer softwareConsultationsConsumptionCustomDataData SetDatabasesDevelopmentEchinoBaseEchinodermataEducational workshopFundingFutureGene ExpressionGenesGenomeGenomic SegmentGenomicsGenus MenthaGoalsGrantHeadHigh-Throughput Nucleotide SequencingIntuitionLinkLiteratureMachine LearningMapsMethodsOrthologous GenePhasePhenotypePhylogenetic AnalysisProcessRegulatory ElementResearchResourcesSiteSpecific qualifier valueSurveysSyntenySystemTechnologyTestingUpdateVariantVisualizationVisualization softwareWritingXenBasebasebiomedical scientistdata accessdata exchangedata modelingdata resourcedata reusedatabase querydatabase schemadesignempowermentflexibilitygenome browsergenome resourcegenome-wideimprovedknowledgebasemembermiddlewaremigrationnew technologynovelparalogous genesingle cell technologysingle-cell RNA sequencingsoftware developmentsymposiumtechnology developmenttooltranscriptome sequencingusabilityweb appweb interfaceweb portal
项目摘要
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.
技术开发概要
增强Echinobase的软件开发
技术开发组件描述Echinobase的软件开发。其中包括
数据库、网络应用程序、用户和管理员界面。新的数据类型和新的策展工作需要
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
社区成员通过我们的门户网站浏览和查询数据。我们最近增加了许多新的
内容类型和特点,以海胆,包括多物种的支持,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的支持
团队,包括GEO管道,单细胞组学,直向同源GO术语,整合paradox基因数据的工具
和更多.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。这是一个很好的例子,说明我们计划如何
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、直观和交互式的Web界面查看、交互和理解RNA-seq数据。
在接下来的五年里,我们将为我们旨在支持的每种新类型的数据采取许多步骤:
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
通过年度调查和会议研讨会与棘皮动物研究界协商,
从我们的科学顾问委员会和合作者,并在未来,在与联盟的协商,
基因组资源(AGR)工作组和其他外部资源,如NCBI和UCSC。计划
新的项目包括来自GEO的ATAC-seq数据,来自DIOPT的paramount数据,单细胞RNA-seq,支持
全基因组CRE预测和计算的表达表型。技术开发也将
支持我们将机器学习应用于Echinobase文献和内容策展。
目标1.支持扩展和新颖的内容。
目标二。生成自定义内容并支持变量和单单元格数据集。
目标3。与外部资源的接口。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
数据更新时间:{{ journalArticles.updateTime }}
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
PETER D VIZE其他文献
PETER D VIZE的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('PETER D VIZE', 18)}}的其他基金
Computational Support for All Echinobase Objectives
对所有 Echinobase 目标的计算支持
- 批准号:
10715582 - 财政年份:2023
- 资助金额:
$ 17.52万 - 项目类别:
Computational Support for All Echinobase Objectives
对所有 Echinobase 目标的计算支持
- 批准号:
10442597 - 财政年份:2018
- 资助金额:
$ 17.52万 - 项目类别:
Computational Support for All Echinobase Objectives
对所有 Echinobase 目标的计算支持
- 批准号:
10241293 - 财政年份:2018
- 资助金额:
$ 17.52万 - 项目类别:
Xenbase: a Xenopus Model Organism Knowledgebase
Xenbase:非洲爪蟾模型生物知识库
- 批准号:
10404996 - 财政年份:2010
- 资助金额:
$ 17.52万 - 项目类别:
Xenbase: a Xenopus Model Organism Knowledgebase
Xenbase:非洲爪蟾模型生物知识库
- 批准号:
10674802 - 财政年份:2010
- 资助金额:
$ 17.52万 - 项目类别:
Xenbase: a Xenopus Model Organism Database
Xenbase:非洲爪蟾模式生物数据库
- 批准号:
8471740 - 财政年份:2010
- 资助金额:
$ 17.52万 - 项目类别:
Xenbase: a Xenopus Model Organism Database
Xenbase:非洲爪蟾模式生物数据库
- 批准号:
8678968 - 财政年份:2010
- 资助金额:
$ 17.52万 - 项目类别:
Xenbase: a Xenopus Model Organism Database
Xenbase:非洲爪蟾模式生物数据库
- 批准号:
7869674 - 财政年份:2010
- 资助金额:
$ 17.52万 - 项目类别:
Xenbase: a Xenopus Model Organism Database
Xenbase:非洲爪蟾模式生物数据库
- 批准号:
8292203 - 财政年份:2010
- 资助金额:
$ 17.52万 - 项目类别:
Cloud implementation of Xenbase the Xenopus model organism knowledgebase
Xenbase Xenopus模型生物知识库的云实现
- 批准号:
10824813 - 财政年份:2010
- 资助金额:
$ 17.52万 - 项目类别:
相似海外基金
CAREER: Efficient Algorithms for Modern Computer Architecture
职业:现代计算机架构的高效算法
- 批准号:
2339310 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Continuing Grant
CAREER: Creating Tough, Sustainable Materials Using Fracture Size-Effects and Architecture
职业:利用断裂尺寸效应和架构创造坚韧、可持续的材料
- 批准号:
2339197 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Standard Grant
Travel: Student Travel Support for the 51st International Symposium on Computer Architecture (ISCA)
旅行:第 51 届计算机体系结构国际研讨会 (ISCA) 的学生旅行支持
- 批准号:
2409279 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Standard Grant
Understanding Architecture Hierarchy of Polymer Networks to Control Mechanical Responses
了解聚合物网络的架构层次结构以控制机械响应
- 批准号:
2419386 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Standard Grant
I-Corps: Highly Scalable Differential Power Processing Architecture
I-Corps:高度可扩展的差分电源处理架构
- 批准号:
2348571 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Standard Grant
Collaborative Research: Merging Human Creativity with Computational Intelligence for the Design of Next Generation Responsive Architecture
协作研究:将人类创造力与计算智能相结合,设计下一代响应式架构
- 批准号:
2329759 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Standard Grant
Hardware-aware Network Architecture Search under ML Training workloads
ML 训练工作负载下的硬件感知网络架构搜索
- 批准号:
2904511 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Studentship
The architecture and evolution of host control in a microbial symbiosis
微生物共生中宿主控制的结构和进化
- 批准号:
BB/X014657/1 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Research Grant
NSF Convergence Accelerator Track M: Bio-Inspired Surface Design for High Performance Mechanical Tracking Solar Collection Skins in Architecture
NSF Convergence Accelerator Track M:建筑中高性能机械跟踪太阳能收集表皮的仿生表面设计
- 批准号:
2344424 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Standard Grant
RACCTURK: Rock-cut Architecture and Christian Communities in Turkey, from Antiquity to 1923
RACCTURK:土耳其的岩石建筑和基督教社区,从古代到 1923 年
- 批准号:
EP/Y028120/1 - 财政年份:2024
- 资助金额:
$ 17.52万 - 项目类别:
Fellowship