The BioCyc Metabolic Network Explorer.
The BioCyc Metabolic Network Explorer.
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DOI：
10.1186/s12859-021-04132-5
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发表时间：
2021-04-21
影响因子：
3
通讯作者：
Karp PD
中科院分区：
文献类型：
--
作者：
Paley S;Karp PD
代谢网络浏览器是BioCyc.org网站和Pathway Tools软件套件的新成员，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只显示所有可能的代谢物连接的子集，否则结果在视觉上会令人不知所措。现有的工具，即使是那些声称显示生物体的完整代谢网络的工具，也会根据预定义的途径或其他预先选择的标准限制显示的连接集。相反，我们试图提供一个工具，让用户动态控制要遵循的连接。代谢网络浏览器是一个易于使用的，基于网络的软件工具，允许用户指定感兴趣的起始代谢物，并在任意方向或两个方向上交互式地探索其直接代谢邻域到任何所需的深度，让用户从完整的连接反应中进行选择。尽管对于其他工具，一次只能看到代谢网络的一小部分，但该部分由用户基于完整的反应补体来选择，并且很容易在感兴趣的替代路径之间切换。显示是直观的，可定制的，并提供了丰富的链接到更详细的信息页面。代谢网络浏览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。它的主要优势是易于使用，生物学家直观的图表，以及与BioCyc Pathway/Genome Database提供的更广泛的数据库的集成。
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. 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. 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.
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影响因子：
14.9
作者：
Jeske L;Placzek S;Schomburg I;Chang A;Schomburg D
通讯作者：
Schomburg D
影响因子：
14.9
作者：
Jewison T;Su Y;Disfany FM;Liang Y;Knox C;Maciejewski A;Poelzer J;Huynh J;Zhou Y;Arndt D;Djoumbou Y;Liu Y;Deng L;Guo AC;Han B;Pon A;Wilson M;Rafatnia S;Liu P;Wishart DS
通讯作者：
Wishart DS
影响因子：
14.9
作者：
Fabregat A;Jupe S;Matthews L;Sidiropoulos K;Gillespie M;Garapati P;Haw R;Jassal B;Korninger F;May B;Milacic M;Roca CD;Rothfels K;Sevilla C;Shamovsky V;Shorser S;Varusai T;Viteri G;Weiser J;Wu G;Stein L;Hermjakob H;D'Eustachio P
通讯作者：
D'Eustachio P
影响因子：
4.1
作者：
Paley S;Billington R;Herson J;Krummenacker M;Karp PD
通讯作者：
Karp PD
途径拼贴：个性化的多条道图。
影响因子：
3
作者：
Paley S;O'Maille PE;Weaver D;Karp PD
通讯作者：
Karp PD