Abstract
BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.
Highlights
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
The Metabolic Network Explorer fills a gap in the existing modes of exploration, enabling the user to begin at a starting metabolite and interactively explore the metabolic neighborhood around that starting point by moving forward and backward in the
All the potential predecessor or successor metabolites of a given metabolite are collected into a single list displayed to the left or right of each central metabolite, minimizing diagram clutter
Summary
The result is a tool that enables easy, interactive browsing of a portion of the metabolic network. Unlike other more general network visualization tools, no prior preselection or preloading of a sub-network is required beyond the initial selection of the database of interest. Limiting the tool to showing only a single linear path at a time allows for a compact, easy-to-read, aesthetically appealing display, but full predecessor and successor metabolite lists visible for every metabolite in the selected path make it easy to identify and explore alternate paths. Ready access to detailed information pages for the reactions, pathways and enzymes associated with the current path provides important context
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