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

霍普学院获得了一笔拨款，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：http://rast.nmpdr.org）是一个基因组注释服务，可以生成高质量的细菌和古细菌基因组注释，以及详细的代谢重建。该基金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)生成和改进基因组规模的代谢反应网络；(2)基于基因组的转录调控预测；(3)基因表达芯片数据分析及调控网络预测。鉴于基因组测序和大规模基因组数据集的生成速度不断加快，生物信息学社区面临的一个主要挑战是提供能够快速、高质量基因组注释和支持高效、集成数据分析的工具。扩展的RAST服务器将为广泛的用户群体提供一套集成的工具，使基因组和高通量转录数据的复杂分析能够比在不同位置使用不同接口的不同工具更有效地完成。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准备，并将利用霍普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开展。

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.