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



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,, 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.

2005-09-01 to 2008-08-31
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