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

• 批准号: 7902169
• 负责人: CATHERINE A BALL
• 金额: $ 112.23万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 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/7902169
• 关键词: Alleles; Animal Model; Arts; 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; Universities; Vision; analytical tool; base; beneficiary; chromatin immunoprecipitation; comparative; comparative genomics; computerized tools; cost; 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

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）：可以说是地球上最好的生物，大肠杆菌既是测试床，又是遗传解剖的受益者，蛋白质和代谢物，分子生物学操纵和进化实验的生化研究。最近，大肠杆菌还被研究并用于开发基因组学和系统生物学的快速前进的工具，从而导致数据和计算工具的迅速增加。尽管大肠杆菌在发现基本的生物学真理和开发开创性的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社区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Web资源Ecolihub2.0。 ecolihub2.0将团结起来并扩展几个现有的软件平台以提供：1）一种强大而直观的用户界面，专为生物学家设计，并使用软件工程的最佳实践，2）无缝访问Art工具的高通量“ OMICS”数据，3），3）科学文献的专家BACIA，以及其他E. coliia coliia and e. coliicia and Ise e. coliia，4）沙门氏菌，5）使用进化关系来检查其他模型生物，肠细菌病原体和人类生物医学条件，6）与大肠杆菌的系统生物学工具相结合，7）扩展和进一步整合基于社区的注释，以基于社区的注释和主要的教育材料来源。 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。得益于进化论和NIH对英镑研究的半个世纪投资，这种微生物继续向我们传授有关所有生命常见的基本细胞过程，从有益和有害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技术，提供具有成本效益的机制，这些机制可用于管理许多NIH赞助的项目的不同专家和资源的协调。