Comparative Analysis of Mycoplasma Bacteria Models Using the CytoSEED Plugin for Metabolic Model Visualization
Dr. Matthew DeJongh
We created digital metabolic models for 4 species of Mycoplasma bacteria using the Model SEED pipeline. We then refined these models based on available experimental data for the 4 species found in various literature sources. The four models are relatively similar, but 217 reactions exist in at least 1 of the 4 models but not in all 4. We also created software tools to both automate parts of the model optimization process as well as to assist us and other scientists in visualizing models. Our CytoSEED plugin for Cytoscape allows dynamic viewing, manipulating, and analyzing of metabolic models created using the Model SEED. Extensions this summer include increased support for viewing gene expression data, the ability to quickly synchronize the visualization of a model when it has been modified, and the ability to import and display the results of flux balance analysis experiments. Additional software tools were built into the Model SEED for model optimization and analysis using gene expression data.
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