Matlab-based visualization analysis of genome-scale metabolic network model simulation of Yarrowia lipolytica

Abstract:

[Objective] In recent decade, genome-scale metabolic network model (GSMM) has been flourishing rapidly. It has been an indispensable tool to investigate complex physiology of organisms through reconstruction of GSMMs and prediction cellular characteristics based on computational simulation. Visualization of simulation results can help to trace intuitively metabolic flux changes in the model and generate possible metabolic engineering strategies. [Methods] In this study, we first briefly summarized current methods for metabolic network visualization, followed by proposing a new method to realize visualization of GSMMs simulation based on Matlab. A pre-drawing of the metabolic network was performed first via CellDesigner software. Two functions of RAVEN toolbox were employed to integrate the raw map into Matlab and to realize visualization of simulation. [Results] As an example, the visualization of iYL619_PCP v1.7, a GSMM of Yarrowia lipolytica was realized. [Conclusion] According to the maps of visualization, we could monitor clearly flux changes in pathways under different environmental and genetic conditions to analyze efficiently simulation results.

Key words:Genome-scale metabolic network model, Yarrowia lipolytica, Visualization, CellDesigner, RAVEN toolbox