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

爱荷华州立大学获得一项资助，开发一个开源集成软件平台MetNet，用于拟南芥系统生物学背景下实验数据和代谢网络的可视化和分析。为了增加我们对特定基因功能的理解并扩大我们对拟南芥的理解，我们需要能够在已知代谢网络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源软件工具的试验版本。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形理论计算（FCModeler）、具有统计分析功能的独特多元显示和分析工具（GeneGobi）、使用开源统计分析语言R进行图形建模和通用文本挖掘（PathBinderA）。它还将增强拟南芥代谢和调控网络数据库，以扩大途径信息并使其可在网上访问。这些工具将能够在代谢和发育网络的背景下放置实验数据，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中进行评估和验证，即拟南芥中的氧化应激网络，作为概念验证。MetNet软件将为研究社区的开源软件工具箱做出贡献。将举办关于如何使用MetNet分析复杂数据集的讲习班。来自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NSF-REU中心的“分子生物技术和基因组学”，那些目前没有机会在本国机构参与研究的科学本科生将参与研究。拓展工作还将包括通过NSF-RET项目接待高中生物教师。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教师实习生的机会。外展将包括Meta！Blast，一个具有综合代谢功能的动态虚拟现实细胞。这个正在进行的项目旨在让年轻学生进入并探索植物细胞的新陈代谢。到目前为止，它完全是由大学生开发的。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。该项目网站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，也将免费提供给感兴趣的学术研究人员。

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.