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

描述（由申请人提供）：可以说是地球上研究得最好的生物体，大肠杆菌一直是遗传解剖、蛋白质和代谢物的生化研究、分子生物学操作和进化实验的试验台和受益者。最近，E。大肠杆菌也被研究并用于开发基因组学和系统生物学的快速发展的工具，导致用于其分析的数据和计算工具的快速增加。尽管E.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发挥了重要作用，但仍然没有在线数据资源满足大肠杆菌多样化和复杂的需求。大肠杆菌研究社区。为了支持这个大型研究社区的需求，我们建议建立下一代网络资源，EcoliHub2.0。EcoliHub2.0将整合并扩展几个现有的软件平台，以提供：1）为生物学家设计的功能强大且直观的用户界面，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”数据工具，3）对常用实验室E.大肠杆菌的比较基因组学工具;大肠杆菌和其他肠道细菌如沙门氏菌，5）使用进化关系来检查其他模式生物，肠道细菌病原体和人类生物医学条件，6）与系统生物学工具的整合，用于大肠杆菌。7）扩展和进一步整合EcoliWiki，用于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。多亏了进化和NIH对磅杆菌研究的半个世纪的投资，这种微生物继续向我们传授所有生命共同的基本细胞过程，从有益和有害的细菌到健康和患病的人类。EcoliHub2.0还将推进基因组数据资源的最新发展，提供具有成本效益的机制，可用于管理NIH赞助的许多项目的不同专家和资源的协调。

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.