MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks

James J. Kelley; Shay Maor; Min Kyung Kim; Anatoliy Lane; Desmond S. Lun

doi:10.1093/bioinformatics/btx240

MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks

James J. Kelley, Shay Maor, Min Kyung Kim, Anatoliy Lane, Desmond S. Lun

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Summary: Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii).

Availability and Implementation: MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/.

Contact: dslun@rutgers.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

Original language	English (US)
Pages (from-to)	2596-2597
Number of pages	2
Journal	Bioinformatics (Oxford, England)
Volume	33
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/btx240
State	Published - Aug 15 2017

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btx240

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title = "MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks",

abstract = "Summary: Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii).Availability and Implementation: MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/.Contact: dslun@rutgers.edu.Supplementary information: Supplementary data are available at Bioinformatics online.",

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AU - Lun, Desmond S.

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