1. MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG
- Author
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Elaine Holmes, Jeremy K. Nicholson, Joram M. Posma, and Steven L. Robinette
- Subjects
Statistics and Probability ,Internet ,Genome ,Computer science ,Systems Biology ,computer.software_genre ,Applications Notes ,Biochemistry ,Toolbox ,Computer Science Applications ,Set (abstract data type) ,Computational Mathematics ,Computational Theory and Mathematics ,Metabolomics ,Graph (abstract data type) ,Data mining ,KEGG ,MATLAB ,Molecular Biology ,Gene ,computer ,Software ,computer.programming_language - Abstract
Summary: MetaboNetworks is a tool to create custom sub-networks in Matlab using main reaction pairs as defined by the Kyoto Encyclopaedia of Genes and Genomes and 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 edited and explored interactively. Furthermore, nodes and edges in the graph are linked to the Kyoto Encyclopaedia of Genes and Genomes compound and reaction pair web pages. Availability and implementation: MetaboNetworks is available from http://www.mathworks.com/matlabcentral/fileexchange/42684. Contact: jmp111@ic.ac.uk or j.nicholson@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
- Published
- 2013
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