EcoliHub2.0: A next-generation E. coli model organism resource (SRI Proposal ECU

EcoliHub2.0：下一代大肠杆菌模型生物资源（SRI提案ECU

基本信息

批准号：
8141954
负责人：
CATHERINE A BALL
金额：
$ 108.63万
依托单位：
UNIVERSITY OF SOUTHERN CALIFORNIA
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-08-01 至 2013-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8141954
关键词：
Alleles Animal Model Bacteria Beds Biochemical Biological Biological Models Cell physiology Communities Computer software DNA Sequence Data Data Set Data Sources Databases Deposition Development Dissection Documentation Education Education and Outreach Educational Curriculum Educational Materials Educational process of instructing Educational workshop Electronics Enteral Enterobacteriaceae Escherichia coli Eukaryota Evolution Family Feeds Galaxy Gene Family Gene Rearrangement Genes Genetic Genome Genomics Health Human Institution International Internet Investments Joints Laboratories Life Link Literature Metabolic Pathway Microbe Molecular Biology Ontology Organism Pathway interactions Persons Phenotype Phylogenetic Analysis Principal Investigator Prokaryotic Cells Proteomics Publications Publishing Relative (related person)Research Research Infrastructure Research Personnel Research Support Resource Development Resources Salmonella Scientist Services Societies Software Engineering Software Tools Source System Systems Biology Technology Testing Texas Training Transcript Trees United States National Institutes of Health Universities Vision analytical tool base beneficiary chromatin immunoprecipitation comparative comparative genomics computerized tools cost effective design genome database improved markov model models and simulation new technology news next generation outreach pathogen protein metabolite protein profiling protein protein interaction public health relevance relational database research study symposium tool user-friendly web-based social networking wiki

项目摘要

DESCRIPTION (provided by applicant): Arguably the best-studied organism on earth, the bacterium Escherichia coli has been both the test bed and the beneficiary of genetic dissections, biochemical studies of proteins and metabolites, molecular biology manipulations and evolutionary experiments. More recently, E. coli has also been studied by and used to develop the rapidly advancing tools of genomics and systems biology, leading to a rapidly increasing body of data and computational tools for its analysis. Despite the critical importance of E. coli in uncovering fundamental biological truths and developing groundbreaking new technologies, there is still no online data resource that satisfies the diverse and sophisticated needs of the E. coli research community. To support the needs of this large research community, we propose to build the next generation web resource, EcoliHub2.0. EcoliHub2.0 will bring together and extend several existing software platforms to provide: 1) a powerful and intuitive user interface designed for biologists and using best practices of software engineering, 2) seamless access to state of the art tools for high-throughput "omics" data, 3) expert curation of the scientific literature for commonly-used laboratory strains of E. coli, 4) powerful comparative genomics tools for E. coli and other enteric bacteria such as Salmonella, 5) use of evolutionary relationships to examine other model organisms, enteric bacterial pathogens, and human biomedical conditions, 6) integration with systems biology tools for E. coli, 7) extension and further integration of EcoliWiki for community-based annotation and primary source for educational materials. Public Health Relevance: The EcoliHub2.0 resource will promote human health by supporting research on a key model system. Thanks to evolution and the NIH's half-century of investment in pound coli research, this microbe continues to teach us about basic cellular processes common to all life, from beneficial and harmful bacteria to healthy and diseased humans. EcoliHub2.0 will also advance the state of the art for genome data resources, providing cost-effective mechanisms that can be applied to the managing the coordination of diverse experts and resources for many NIH-sponsored projects.

描述（由申请人提供）：大肠杆菌可以说是地球上研究得最好的生物体，它既是基因解剖、蛋白质和代谢物生化研究、分子生物学操作和进化实验的试验台，也是受益者。最近，大肠杆菌也被研究并用于开发快速发展的基因组学和系统生物学工具，导致用于其分析的数据和计算工具迅速增加。尽管大肠杆菌在揭示基本生物学真理和开发突破性新技术方面至关重要，但仍然没有在线数据资源可以满足大肠杆菌研究界多样化和复杂的需求。为了支持这个大型研究社区的需求，我们建议构建下一代网络资源 EcoliHub2.0。 EcoliHub2.0 将汇集并扩展多个现有软件平台，以提供：1）为生物学家设计的强大而直观的用户界面，并使用软件工程的最佳实践，2）无缝访问最先进的高通量“组学”工具“数据，3) 专家整理的常用实验室大肠杆菌菌株的科学文献，4) 大肠杆菌和沙门氏菌等其他肠道细菌的强大比较基因组学工具，5) 利用进化关系检查其他模式生物、肠道细菌病原体和人类生物医学状况，6) 与大肠杆菌系统生物学工具集成，7) 扩展和进一步集成 EcoliWiki，以实现基于社区的注释和教育材料的主要来源。公共卫生相关性：EcoliHub2.0 资源将通过支持关键模型系统的研究来促进人类健康。由于进化和美国国立卫生研究院半个世纪以来对大肠杆菌研究的投资，这种微生物继续向我们传授所有生命共有的基本细胞过程，从有益和有害的细菌到健康和患病的人类。 EcoliHub2.0 还将推动基因组数据资源的发展，提供具有成本效益的机制，可应用于管理许多 NIH 资助项目的不同专家和资源的协调。