SAMMI：一种用于代谢网络可视化的半自动化工具。
SAMMI: a semi-automated tool for the visualization of metabolic networks.
机构信息
Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
出版信息
Bioinformatics. 2020 Apr 15;36(8):2616-2617. doi: 10.1093/bioinformatics/btz927.
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.
摘要
本文介绍了一种基于浏览器的半自动代谢图绘制工具（SAMMI），用于代谢网络的可视化。该工具的自动化功能可轻松实现网络分区、导航和节点定位，同时也提供了广泛的手动地图编辑功能。这种组合可以快速、特定于上下文的方式可视化代谢网络，并开发标准化的、大规模的、具有吸引力的地图。SAMMI 的实现与流行的基于约束的建模工具箱相结合，还可以轻松可视化基因组规模代谢模型的模拟结果。
可用性和实现
SAMMI 已作为独立的基于网络的工具以及 COBRA 和 COBRApy 工具箱的插件实现。SAMMI 及其 COBRA 插件根据 GPL 3.0 许可证获得许可，并可在 www.SammiTool.com 上获得文档、教程和源代码。
补充信息
补充数据可在Bioinformatics 在线获得。
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