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Joram Posma


18 Jul 2013 (Updated )

A toolbox to interactively create, customize and explore multi-systemic metabolic reaction networks

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A Matlab-based tool to create custom sub-networks using main substrate-product pairs as defined by the Kyoto Encyclopaedia of Genes and Genomes (KEGG). It can be used to explore transgenomic interactions, for example mammalian and bacterial associations. It calculates the shortest path between a set of metabolites (e.g. biomarkers from a metabonomic study) and plots the connectivity between metabolites as links in a network graph. The resulting graph can be changed and explored interactively. Furthermore, nodes in the graph are linked to the KEGG compound webpage.

A multi-systemic example data set is provided of a supra-organism, this includes reactions that can occur in compartments of homo sapiens, firmicutes and/or bacretoidetes species. The MetaboGetworks function can be used to generate custom multi-organism databases to use in the MetaboNetworks function. (See the READ ME file)

Required Products MATLAB
MATLAB release MATLAB 7.14 (R2012a)
Other requirements Platform dependence: none found (tested on Windows 7, Mac OSX 7.14 (Snow Leopard)) Software dependence: none found (tested on Matlab versions 2010b, 2012a, 2012b, 2013a)
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22 Apr 2014 yysuccess



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22 Jul 2013

Removal of a parfor in the TextMatch code.

03 Sep 2013

Fixed 2 errors in subfunctions of MetaboGetworks, added function descriptions of input and output variables.

16 Sep 2013

2 new functionalities: edges linked to corresponding KEGG reaction pair web page, text edit option to change a specific string (e.g. 'hydroxy' to 'OH') for all nodes simultaneously. Search functions for selecting organisms/metabolites were updated.

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