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Project details

Modeling Bacterial Metabolism and Genetic Regulation

Project Full Title:

Systems Biology: creating computer models of bacterial metabolism and genetic regulation

Project Mentor(s):

Best,Aaron; DeJongh,Matthew

Project Mentor(s) EMail:;

Project Start Date:


Project End Date:


Project Description:

This project involves a team of biology and computer science students and faculty in interdisciplinary research in systems biology. The goal of systems biology is to build computer models that use genetic information about an organism to simulate and predict its behavior. These models are useful for determining how organisms interact with their environment.

Over the past five summers, students involved in this project have developed software to generate metabolic models for the microbial organisms represented in the SEED, a comparative genomics analysis environment ( This summer, we will develop additional tools for refining these models and applying them to systems level analyses.

  • Biology students: We seek students interested in microbiology and biochemistry. We will work closely with the computer science faculty and students, using the tools that they develop to analyze and refine models of particular bacteria. We will provide feedback on how to improve the tools.

  • Computer Science students: We will work with Perl, CGI, Ajax, and Java. Knowledge of molecular biology, microbiology and genetics is helpful but not necessary.

    We anticipate that this project will result in several publications, including the bacterial models developed during the summer, and the software tools and techniques for refining and analyzing them. Students may have opportunities to travel to Argonne National Laboratory and several scientific conferences to present the results of their research.

    This project is funded by the National Science Foundation's programs in Molecular and Cellular Biosciences.

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