Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA.
Nucleic Acids Res. 2020 Jul 2;48(W1):W427-W435. doi: 10.1093/nar/gkaa409.
Next-generation sequencing has paved the way for the reconstruction of genome-scale metabolic networks as a powerful tool for understanding metabolic circuits in any organism. However, the visualization and extraction of knowledge from these large networks comprising thousands of reactions and metabolites is a current challenge in need of user-friendly tools. Here we present Fluxer (https://fluxer.umbc.edu), a free and open-access novel web application for the computation and visualization of genome-scale metabolic flux networks. Any genome-scale model based on the Systems Biology Markup Language can be uploaded to the tool, which automatically performs Flux Balance Analysis and computes different flux graphs for visualization and analysis. The major metabolic pathways for biomass growth or for biosynthesis of any metabolite can be interactively knocked-out, analyzed and visualized as a spanning tree, dendrogram or complete graph using different layouts. In addition, Fluxer can compute and visualize the k-shortest metabolic paths between any two metabolites or reactions to identify the main metabolic routes between two compounds of interest. The web application includes >80 whole-genome metabolic reconstructions of diverse organisms from bacteria to human, readily available for exploration. Fluxer enables the efficient analysis and visualization of genome-scale metabolic models toward the discovery of key metabolic pathways.
下一代测序技术为重建基因组规模的代谢网络铺平了道路，成为理解任何生物体代谢回路的强大工具。然而，从包含数千个反应和代谢物的大型网络中可视化和提取知识是当前需要用户友好工具的挑战。在这里，我们介绍 Fluxer（https://fluxer.umbc.edu），这是一个免费的开源新型 Web 应用程序，用于计算和可视化基因组规模的代谢通量网络。任何基于系统生物学标记语言的基因组规模模型都可以上传到该工具，该工具会自动执行通量平衡分析并计算不同的通量图以进行可视化和分析。主要的代谢途径，无论是生物量生长还是任何代谢物的生物合成，都可以使用不同的布局进行交互式敲除、分析和可视化，作为生成树、树状图或完整图。此外，Fluxer 可以计算和可视化任意两个代谢物或反应之间的 k 最短代谢路径，以确定两个感兴趣化合物之间的主要代谢途径。该 Web 应用程序包含来自细菌到人类的 80 多个不同生物体的全基因组代谢重建，可随时进行探索。Fluxer 能够有效地分析和可视化基因组规模的代谢模型，以发现关键代谢途径。
