Rodeo: A Platform for Discovery and Analysis of Protein Network Motifs

Rodeo：蛋白质网络基序发现和分析的平台

• 批准号: 0543480
• 负责人: Dennis Wall
• 金额: $ 71万
• 依托单位: Harvard University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-15 至 2010-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0543480&HistoricalAwards=false
• 关键词: Rodeo; Platform; Discovery; Analysis; Protein

Harvard University is awarded a grant to build a new publicly available informatics tool, called Rodeo that will allow the integration of data relevant to deciphering protein-protein interaction networks and will provide a number of methods for analyzing such data, including graph-theoretic mathematics. Rodeo will allow the integration and analysis of several databases including a comprehensive set of orthologs from over 50 genomes, a new set of protein-protein (p-p) interaction data from humans together with over 70,000 p-p interactions from other organisms, a massive set of gene expression data from new experiments and experiments hosted by NCBI, and a database of almost 100,000 Expressed Sequence Tags from an organism (the acorn worm) that may hold the key for understanding the developmental complexity which evolved in modern day vertebrate animals. Rodeo will allow the interrogation of data not just from one organism, but across multiple organisms, providing a way to search for convergently evolved patterns a vital step to understanding process. Rodeo will also allow the visualization of motifs to literally 'see' patterns of network complexity. Rodeo will also be a valuable tool for education and research on protein-protein interaction motifs, and a general resource on the application of graph algorithms to complex questions in biology. Rodeo will be made accessible to not just advanced scientists interested in network structures of interactomes, but to any student of biology concerned with learning more about the complexity of the cell. Specifically a training program will be developed consisting of a 2-day training course on 'motif discovery' at Harvard Medical School that will be open to the international scientific community at no cost. This will be co-taught by the PI and senior personnel on the proposal, with introductory lectures on graph models and algorithms for biology, as well as hands-on training with Rodeo. Secondly, a virtual training via the Rodeo web portal will be created that will contain extensive documentation, as well as streaming video of our 'motif discovery' training seminars. Thirdly, Rodeo tutorials will be held at two of the major symposia on biocomputing, which will also be available through the Rodeo web portal. And last not least, Rodeo will be incorporated into the training curriculum for graduate students in the Department of Systems Biology at the Medical School.

哈佛大学获得了一笔赠款，用于建立一个新的公开可用的信息学工具，称为牛仔竞技表演，它将允许整合与破译蛋白质相互作用网络相关的数据，并将提供许多分析这些数据的方法，包括图论数学。牛仔竞技表演将允许整合和分析几个数据库，包括来自50多个基因组的一套全面的直系同源物，一套新的来自人类的蛋白质-蛋白质（p-p）相互作用数据，以及来自其他生物体的70，000多个p-p相互作用数据，来自新实验和NCBI主持的实验的大量基因表达数据，以及一个近100个的数据库，000表达序列标签从一个有机体（橡子蠕虫），可能持有的关键，了解发展的复杂性，在现代脊椎动物进化。牛仔竞技表演将允许不仅仅从一个生物体，而是在多个生物体中询问数据，提供一种寻找趋同进化模式的方法，这是理解过程的重要一步。牛仔竞技表演还将允许图案的可视化，从而从字面上“看到”网络复杂性的模式。牛仔竞技表演也将是一个有价值的工具，为教育和研究蛋白质相互作用的图案，并在生物学中的复杂问题的图形算法的应用一般资源。牛仔竞技表演将不仅提供给对相互作用体网络结构感兴趣的高级科学家，而且提供给任何关心了解更多细胞复杂性的生物学学生。具体而言，将制定一项培训计划，包括在哈佛医学院举办为期2天的“基序发现”培训课程，该课程将免费向国际科学界开放。这将由PI和该提案的高级人员共同授课，包括关于生物学图形模型和算法的介绍性讲座，以及与牛仔竞技表演的实践培训。其次，通过牛仔竞技表演门户网站的虚拟培训将创建，将包含广泛的文件，以及我们的“主题发现”培训研讨会的流媒体视频。第三，将在两个关于生物计算的主要专题讨论会上提供牛仔竞技表演辅导，也可通过牛仔竞技表演门户网站获得。最后，牛仔竞技表演将被纳入医学院系统生物学系研究生的培训课程。