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

爱荷华州立大学获得一笔赠款，用于开发一个开源的集成软件平台MetNet，用于在拟南芥系统生物学的背景下对实验数据和代谢网络进行可视化和分析。为了增加我们对特定基因功能的理解，扩大我们对拟南芥的理解，我们需要能够在有关代谢网络的已知信息的背景下分析不同数据类型的软件。该项目将增强三个新的公开可用的开放源码软件工具的试运行版本。MetNet平台将具有图形可视化和建模、交互式显示、用于确定生物距离的强大图论计算(FCModeler)、具有统计分析功能的独特多变量显示和分析工具(GeneGobi)、使用开源统计分析语言R的图形建模以及多功能文本挖掘(PathBinderA)。它还将加强拟南芥代谢和调控网络的数据库，以扩大途径信息并使其可在网上访问。这些工具将能够将实验数据放在新陈代谢和发育网络的背景下，以提出关于拟南芥基因功能的新见解。该软件将在一个测试案例--拟南芥的氧化应激网络--上进行评估和验证，作为概念的证明。MetNet软件将为研究社区的开源软件工具箱做出贡献。将就如何使用MetNet分析复杂的数据集举办讲习班。生物学家用户的评价将提供改进的反馈。通过积极参与爱荷华州立大学NSF-REU中心的“分子生物技术和基因组学”，目前没有机会在本国机构参与研究的理科本科生将参与到这项研究中来。外展还将包括通过NSF-RET计划接待高中生物教师。MetNet是一个多学科项目，将为研究生和博士后研究人员提供指导本科生和实习生的机会。扩展范围将包括Meta！BLAST，这是一种具有集成新陈代谢的动态虚拟现实细胞。这个正在进行的项目旨在让年轻的学生进入并探索植物细胞的新陈代谢。到目前为止，它完全是由本科生开发的。实习生将参与该单元的开发和评估。这些活动将促进研究、教育和向广大受众传播我们的成果，同时培养新一代科学家。项目网站http://www.public.iastate.edu/~mash/MetNet/homepage.html，将向公众开放，并将包含有关该项目、参与者、开发的软件和根据该奖项建立的数据库的信息。数据库和信息将与TAIR共享，感兴趣的学术研究人员也可以免费使用。

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.