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生物代谢网络浏览器。

The BioCyc Metabolic Network Explorer.

机构信息

Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA.

出版信息

BMC Bioinformatics. 2021 Apr 21;22(1):208. doi: 10.1186/s12859-021-04132-5.

DOI:10.1186/s12859-021-04132-5
PMID:33882841
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8060992/
Abstract

BACKGROUND

The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by necessity show only a subset of all possible metabolite connections, or the results will be visually overwhelming. Existing tools, even those that purport to show an organism's full metabolic network, limit the set of displayed connections based on predefined pathways or other preselected criteria. We sought instead to provide a tool that would give the user dynamic control over which connections to follow.

RESULTS

The Metabolic Network Explorer is an easy-to-use, web-based software tool that allows the user to specify a starting metabolite of interest and interactively explore its immediate metabolic neighborhood in either or both directions to any desired depth, letting the user select from the full set of connected reactions. Although, as for other tools, only a small portion of the metabolic network is visible at a time, that portion is selected by the user, based on the full reaction complement, and it is easy to switch among alternate paths of interest. The display is intuitive, customizable, and provides copious links to more detailed information pages.

CONCLUSIONS

The Metabolic Network Explorer fills a gap in the set of metabolic network visualization tools and complements other modes of exploration. Its primary strengths are its ease of use, diagrams that are intuitive to biologists, and its integration with the broader corpus of data provided by a BioCyc Pathway/Genome Database.

摘要

背景

代谢网络探索器是 BioCyc.org 网站和途径工具软件套件的新增功能，支持代谢网络的交互式探索。任何代谢网络可视化工具都必须在必要时仅显示所有可能代谢物连接的子集，否则结果将在视觉上令人不知所措。现有的工具，即使那些声称显示生物体完整代谢网络的工具，也会根据预定义的途径或其他预选标准限制显示连接的集合。相反，我们寻求提供一种工具，使用户能够动态控制要遵循的连接。

结果

代谢网络探索器是一种易于使用的基于网络的软件工具，允许用户指定感兴趣的起始代谢物，并在任意方向上交互探索其直接代谢邻域，达到用户所需的任意深度，使用户可以从完整的连接反应集中进行选择。尽管与其他工具一样，一次只能看到代谢网络的一小部分，但该部分是根据完整的反应补充由用户选择的，并且可以轻松在感兴趣的替代路径之间切换。显示直观、可定制，并提供大量链接以获取更详细的信息页面。

结论

代谢网络探索器填补了代谢网络可视化工具集的空白，并补充了其他探索模式。它的主要优点是易于使用、对生物学家直观的图表以及与由 BioCyc 途径/基因组数据库提供的更广泛数据体的集成。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b90e/8060992/ce9d06d33dce/12859_2021_4132_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b90e/8060992/f314dd6b7c92/12859_2021_4132_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b90e/8060992/ce9d06d33dce/12859_2021_4132_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b90e/8060992/f314dd6b7c92/12859_2021_4132_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b90e/8060992/ce9d06d33dce/12859_2021_4132_Fig2_HTML.jpg

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