Yazdan Asgari*, Zahra Zabihinpour and Ali Masoudi-Nejad Pages 100 - 107 ( 8 )
Background: Modelling and analysis of metabolic networks can be carried out with different levels of granularity, ranging from structural (topological) analysis to constraint-based methods to kinetic modelling. The increasing number of genome-scale metabolic reconstructions and the growing importance of metabolic modelling intensify the need for integrated approaches allowing the application of different analysis methods.
Objective: There is no well-organized and freely accessible code package or specific toolbox/plugin available for the reconstruction of metabolite- and enzyme-centric networks. So, we have developed a toolbox which could be able to perform such reconstructions.
Method: We have developed the SCAN-toolbox, an Add-on to the widely used COBRA framework for constraint-based modelling. SCAN is an open-source MATLAB/Octave toolbox which extends the COBRA framework and provides functions to prepare different metabolite- and enzyme-centric networks that could also be imported in other structural analysis softwares, such as Cytoscape.
Results: We have applied the SCAN-toolbox to four metabolic networks to demonstrate its applicability.
Conclusion: SCAN extends the COBRA framework towards structural analysis of large metabolic networks, including the reconstruction of undirected and directed metabolite- as well as enzyme-centric networks.
Metabolic networks, metabolic modelling, structural analysis, COBRA toolbox, Cytoscape, MATLAB.
School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Department of Chemistry, Kharazmi University, Tehran, Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran