SCAN-Toolbox: Structural COBRA Add-oN (SCAN) for Analysing Large Metabolic Networks

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.