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

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有机体，它既是基因解剖、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，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满足大肠杆菌研究界的多样化和复杂需求。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将汇集和扩展几个现有的软件平台，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)无缝访问高通量“组学”数据的最先进工具，3)大肠杆菌常用实验室菌株的科学文献专家管理，4)大肠杆菌和其他肠道细菌（如沙门氏菌）的强大比较基因组学工具，5)使用进化关系来检查其他模式生物，肠道细菌病原体，6)整合大肠杆菌的系统生物学工具，7)扩展并进一步整合EcoliWiki，用于社区注释和教育材料的主要来源。

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.