SAMMI: A semi-Automated tool for the visualization of metabolic networks

Andre Schultz; Rehan Akbani

doi:10.1093/bioinformatics/btz927

SAMMI: A semi-Automated tool for the visualization of metabolic networks

Andre Schultz, Rehan Akbani

Bioinformatics & Computational Biology

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

3 Scopus citations

Abstract

Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models.

Original language	English (US)
Pages (from-to)	2616-2617
Number of pages	2
Journal	Bioinformatics
Volume	36
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btz927
State	Published - Apr 15 2020

ASJC Scopus subject areas

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

MD Anderson CCSG core facilities

Metabolomics Facility

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10.1093/bioinformatics/btz927

Cite this

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title = "SAMMI: A semi-Automated tool for the visualization of metabolic networks",

abstract = "Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models.",

author = "Andre Schultz and Rehan Akbani",

note = "Funding Information: This work was supported by the grants National Institutes of Health/ National Cancer Institute [U24CA210950, U01CA235510, P30 CA016672 and Department of Defense/Congressionally Directed Medical Research Programs W81XWH-16-1-0237]. Publisher Copyright: {\textcopyright} 2019 The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.",

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doi = "10.1093/bioinformatics/btz927",

language = "English (US)",

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PY - 2020/4/15

Y1 - 2020/4/15

N2 - Here we present a browser-based Semi-Automated Metabolic Map Illustrator (SAMMI) for the visualization of metabolic networks. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps. The implementation of SAMMI with popular constraint-based modeling toolboxes also allows for effortless visualization of simulation results of genome-scale metabolic models.

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SAMMI: A semi-Automated tool for the visualization of metabolic networks

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

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