Arabidopsis 2010: MetNet: Integrated Software for Arabidopsis Systems Biology Research

拟南芥 2010：MetNet：拟南芥系统生物学研究的集成软件

• 批准号: 0520267
• 负责人: Eve Wurtele
• 金额: $ 96.96万
• 依托单位: Iowa State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-01 至 2008-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0520267&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; MetNet; Integrated; Software

Iowa State University is awarded a grant to develop an open source integrated software platform, MetNet, for visualization and analysis of experimental data and metabolic networks in the context of Arabidopsis systems biology. To increase our understanding of the function of specific genes and expand our understanding of Arabidopsis, we need software that enables the analysis of disparate data types in the context of known information about metabolic networks. This project will enhance pilot-versions of three new publicly available, open source software tools. The MetNet platform will feature graph visualization and modeling, interactive displays, powerful graph-theoretic computations for determining biological distances (FCModeler), a unique multivariate display and analysis tool with functionality to do statistical analyses (GeneGobi), graph modeling using the open source statistical analysis language, R, and versatile text mining (PathBinderA). It will also enhance the database of metabolic and regulatory networks in Arabidopsis to expand the pathway information and make it web-accessible. These tools will be able to place experimental data in the context of metabolic and developmental networks to propose new insights about Arabidopsis gene function. The software will be evaluated and validated on a test case, the oxidative stress network in Arabidopsis, as a proof of concept. MetNet software will contribute to the research community's open source software toolbox. Workshops will be conducted on how to analyze complex data sets using MetNet. Evaluations from biologist users will provide feedback for improvements. Through active participation in "Molecular Biotechnology and Genomics" NSF-REU Center at Iowa State University, science-bound undergraduates who currently do not have the opportunity to participate in research at their home institutions, will be involved in the research. Outreach will also include hosting high school biology teachers through the NSF-RET program. MetNet is a multi-disciplinary project that will provide graduate students and postdoctoral researchers opportunities to mentor undergraduate and teacher interns. Outreach will encompass Meta!Blast, a dynamic virtual reality cell with integrated metabolism. This ongoing project is designed to allow young students to enter and explore the metabolism of a plant cell. Thus far it has been developed entirely by undergraduates. Interns will participate in the development and evaluation of this cell. These activities will promote research, education, and dissemination of our results to a broad audience, while developing a new generation of scientists.The project website, http://www.public.iastate.edu/~mash/MetNet/homepage.html, will be open to public and will contain information about the project, participants, developed software, and databases built under this award. The database and information will be shared with TAIR, and will also be freely available to interested academic researchers.

爱荷华州立大学获得赠款，以开发开源的集成软件平台Metnet，以在拟南芥系统生物学的背景下可视化和分析实验数据和代谢网络。为了增强我们对特定基因功能的理解并扩展我们对拟南芥的理解，我们需要在有关代谢网络的已知信息的背景下对不同数据类型进行分析的软件。该项目将增强三种新公开的开源软件工具的试点反应。 MetNet平台将具有图形可视化和建模，交互式显示，功能强大的用于确定生物学距离（FCModeler）的图形理论计算（FCModeler），这是一种具有统计分析功能的唯一多元显示和分析工具（Genegobi），使用开源统计分析语言，R和Versatile Text文本矿山（PathBindera）使用统计分析（Genegobi）。它还将增强拟南芥中代谢和监管网络的数据库，以扩展路径信息并使其可访问。这些工具将能够在代谢和发展网络的背景下放置实验数据，以提出有关拟南芥基因功能的新见解。该软件将在测试用例，拟南芥中的氧化应激网络上进行评估和验证，作为概念证明。 Metnet软件将有助于研究社区的开源软件工具箱。将在如何使用Metnet进行有关如何分析复杂数据集的研讨会。生物学家用户的评估将为改进提供反馈。通过积极参与爱荷华州立大学的“分子生物技术和基因组学” NSF-REU中心，科学结合的本科生目前将没有机会参加其家庭机构的研究，将参与研究。外展还将包括通过NSF-RET计划主持高中生物学老师。 Metnet是一个多学科项目，它将为研究生和博士后研究人员提供指导本科生和教师实习生的机会。外展将涵盖Meta！Blast，这是一种具有整合代谢的动态虚拟现实细胞。该正在进行的项目旨在使年轻学生进入和探索植物细胞的代谢。到目前为止，它完全由大学生开发。实习生将参与该单元的开发和评估。这些活动将在开发新一代科学家的同时促进我们的结果的研究，教育和传播。数据库和信息将与Tair共享，也将向感兴趣的学术研究人员免费获得。