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

Author(s): Yazdan Asgari*, Zahra Zabihinpour, Ali Masoudi-Nejad

Journal Name: Current Bioinformatics

Volume 13 , Issue 1 , 2018


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Abstract:

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.

Keywords: Metabolic networks, metabolic modelling, structural analysis, COBRA toolbox, Cytoscape, MATLAB.

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Article Details

VOLUME: 13
ISSUE: 1
Year: 2018
Published on: 23 November, 2016
Page: [100 - 107]
Pages: 8
DOI: 10.2174/1574893611666161123123729
Price: $65

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