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IPM
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“School of Biological”

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Paper   IPM / Biological / 15569
School of Biological Sciences
  Title:   SCAN-Toolbox: Structural COBRA Add-oN (SCAN) for Analysing Large Metabolic Networks
  Author(s): 
1.  Yazdan Asgari
2.  Zahra Zabihinpour
3.  Ali Masoudi-Nejad
  Status:   Published
  Journal: Current Bioinformatics
  No.:  1
  Vol.:  13
  Year:  2018
  Pages:   100-107 - DOI: https://doi.org/10.2174/1574893611666161123123729
  Supported by:  IPM
  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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