Here, you can find a description of the features available on the search page and visualization page of the Hub Pathways Webserver. The purpose of this webserver is to illustrate the hub search method as described in Kim et al. (in review) and to gather feedback on the search/visualization interface. If you have any feedback or additional questions that are not answered below, please contact us here. The code for the server is available upon request.

Search Page

This is the starting page where new pathfinding searches can be run, and completed pathways results and example search results can be selected to be viewed in the visualization page.

Example Searches

Example searches are search results that can be visualized right away, without having to run a search and wait for the results to be returned (running a search is explained in a later section).
The example searches are based on the test set of start and end compounds used in Kim et al. (in review). The following information is provided for each search result:

  • Start:Start compound
  • Target:Target compound being synthesized
  • Algorithm:The search algorithm used to find the pathway results. This can be LPAT (described in Heath et al. 2011) or HPAT (described in Kim et al. - in review.)
  • Hub Table:This is the table of all precomputed pathways between a selected set of hub compounds. HubT_out_50 is the hub table that uses the 50 compounds with the highest out-degree (number of reactions that use the compound as a reactant), based on the KEGG reactions database. This hub table was used in the Kim et al. paper (in review).

  • To go to the visualization of a search result, click the "View" button under the "Results" column.

    Run a New Search

    To run a new search, you must specify the following configurations:

    Once these configurations have been set, click the "Execute pathway search" button to run the search. When the search is completed, the results will appear in the "Search Results" section.

    Search Results

    The search results are displayed in the same format as the example searches. After running a search (as described above), the results (if any) will be displayed in this section.



  • Green node: start compound
  • Red node: goal compound
  • Gray node: intermediary compounds
  • Solid edge: reaction edge between compounds
  • Dashed edge: represents an abstraction of multiple pathways between two hub compounds. Click to expand and view hub-to-hub pathways.
  • Controls

  • Click on a node to view more information about that compound in the info panel (left sidebar)
  • Click on a hub link (dashed edge between yellow nodes) to view all the pathways between the two hub compounds
  • Right-click or CTRL+click on a node to view filtering options for that node
  • Click and drag on the canvas (gray background) to move the viewport
  • Click and drag a node to move it around and fix its location.
  • Double click a fixed-position node to release it
  • Scroll on the canvas to zoom in and out

  • Filtering

    On the left side bar, there are options for finding and filtering pathways.


  • Search for compounds: Specific compounds in the visualization can be highlighted by searching for the compound's name or KEGG ID. Click on the dropdown box and start typing to search for a specific compound. Once a compound is selected, the corresponding compound node in the visualization will be highlighted.

  • Filter