Extending the RAST Server to Support Reconstruction and Modeling of Cellular Networks

扩展 RAST 服务器以支持蜂窝网络的重建和建模

• 批准号: 0850546
• 负责人: Matthew DeJongh
• 金额: $ 126.72万
• 依托单位: Hope College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0850546&HistoricalAwards=false
• 关键词: Extending; RAST; Server; Support; Reconstruction

Hope College is awarded a grant to extend the Rapid Annotation using Subsystem Technology (RAST) genome annotation server to support reconstruction and modeling of cellular networks. The RAST server (online at http://rast.nmpdr.org), is a genome annotation service that produces high-quality annotations of bacterial and archaeal genomes, along with a detailed metabolic reconstruction. This grant supports the development of software tools to enable three types of analyses that will be integrated into the RAST server: (1) generation and refinement of genome-scale metabolic reaction networks; (2) genome-based prediction of transcriptional regulons; and (3) analysis of gene expression microarray data and regulatory network prediction. A major challenge facing the bioinformatics community in view of the ever increasing pace of genome sequencing and generation of large-scale genome-based data sets is to provide tools that enable rapid, high-quality genome annotations and support efficient, integrated data analyses. The extended RAST server will provide a broad user community with an integrated suite of tools that enables sophisticated analyses of genomic and high throughput transcription data to be accomplished more efficiently than would be possible using disparate tools in different locations with different interfaces. This project will provide undergraduate students in biology and computer science with hands-on experience in interdisciplinary research that will prepare them for graduate work or other scientific activity, and will draw on Hope College's existing collaborations with area community colleges and the local public school system to provide research opportunities to students from underrepresented groups in the sciences. The project will be carried out in collaboration with the Fellowship for Interpretation of Genomes, and Burnham Institute for Medical Research.

希望学院获得拨款，用于扩展使用子系统技术 (RAST) 基因组注释服务器的快速注释，以支持蜂窝网络的重建和建模。 RAST 服务器（在线网址为 http://rast.nmpdr.org）是一种基因组注释服务，可生成细菌和古细菌基因组的高质量注释以及详细的代谢重建。 这笔赠款支持软件工具的开发，以实现将集成到 RAST 服务器中的三种类型的分析：（1）基因组规模代谢反应网络的生成和完善； (2)基于基因组的转录调节子预测； (3)基因表达微阵列数据分析和调控网络预测。鉴于基因组测序和大规模基因组数据集生成的步伐不断加快，生物信息学界面临的一个主要挑战是提供能够快速、高质量基因组注释并支持高效、集成数据分析的工具。 扩展的 RAST 服务器将为广泛的用户社区提供一套集成的工具，与在不同地点使用不同界面的不同工具相比，能够更有效地完成基因组和高通量转录数据的复杂分析。该项目将为生物学和计算机科学专业的本科生提供跨学科研究的实践经验，为他们的研究生工作或其他科学活动做好准备，并将利用希望学院与地区社区学院和当地公立学校系统的现有合作，为来自科学领域代表性不足群体的学生提供研究机会。该项目将与基因组解释奖学金和伯纳姆医学研究所合作进行。