CytoSEED: Software for Viewing and Analyzing Bacterial Metabolic Models

Faculty Mentor(s)

Dr. Matt DeJongh, Hope College

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The goal of our research is to develop software that will help biologists to better understand and visualize the metabolic pathways of bacteria. A metabolic pathway is a group of compounds and reactions involved in a specific biological process. The Model SEED project currently provides a static viewer for bacterial metabolic pathways. However, this viewer does not support editing pathways - in particular adding, removing, and moving nodes that represent reaction`s and compounds to different pathways. The software we have developed addresses this shortcoming by replicating the capabilities of the current viewer and allowing modifications to the metabolic pathways. These modifications include the ability to move reactions and compounds between existing and newly created pathways. We have also implemented the ability to view multiple bacterial models simultaneously so biologists can easily compare pathways to comprehend differences between bacteria. A goal of this project has also been to take the information that is available within the Model SEED and display it in a more accessible way. This is done through node coloration and connections as well as displaying information inside panels. Our software enables biologists to view data from gene expression experiments by superimposing them on pathways using node coloration. Biologists can use information provided by our software to design laboratory experiments that test bacterial metabolism under specific conditions and view the results. These capabilities enable biologists to gain more knowledge about bacteria relevant to human health, energy production, and environmental impact.


This research was supported by the NSF grants 0745100 and 0850546.

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