Work

SAMMI: a semi-automated tool for the visualization of metabolic networks

Year: 2019

Type: article

Abstract: SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: SAMMI has been implemented as a standalone web-based tool and as plug-ins for the COBRA and COBRApy toolboxes. SAMMI and its COBRA plugins are available under the GPL 3.0 license and are available along with documentation, tutorials, and source code at www.SammiTool.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btz927

Authors: Andre Schultz, Rehan Akbani

Institution: The University of Texas MD Anderson Cancer Center

Language: English

Topic: Microbial Metabolic Engineering and Bioproduction

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Institutes of Health, National Cancer Institute

Awards: G111615301, G3021679957, G3372187468, G631823652, Cancer Center Support Grant