Help

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:

• Algorithm:The search algorithm used to find the pathway results. This can be LPAT (described in Heath et al. 2011) or Hub Search / HPAT (described in Kim et al. - in review.)
• Start:Start compound
• Target:Target compound being synthesized
• Hub Database:This is the table of all precomputed pathways between a selected set of hub compounds. You have the following options:
  • 20 Hubs (Out-Degree): Hub compounds are the 20 compounds with the higest out-degree (number of reactions that use the compound as a reactant)
  • 50 Hubs (Out-Degree): Hub compounds are the 50 compounds with the higest out-degree (number of reactions that use the compound as a reactant)
  • 50 Hubs (In-Degree): Hub compounds are the 50 compounds with the higest in-degree (number of reactions that produce the compound as a product)
  • 50 Hubs (Degree): Hub compounds are the 50 compounds with the higest degree (number of reactions that involve this compound as a reactant or product)
  • 139 Hubs (Araki et al. 2015): Hub compounds are the 139 hub compounds identified by Araki et al. 2015.
• Carbon tracking: How carbons will be tracked in the search. You have the following options:
  • Max: Track the maximum number of carbon atoms possible throughout the search.
  • One: Track at least one carbon atom throughout the search.
  • None: Do not track carbon atoms.
• Allow Reversible Reactions: If checked, all reactions will be considered reversible. If this is not checked, the reversibility of a reaction will be determined by KEGG reaction directionality.

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.

Visualization

Legend

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.

Find

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

• Exclude pathways containing specific compound(s):Pathways can be filtered out based on the compounds cotained / not contained in the pathway. To filter out all pathways that contain a specific compound, you can either:
  1. Right click a compound node: Right click a compound node, then choose to exclude all pathways that contain the compound.
  2. Enter the KEGG id in the filter options:Under the "Exclude pathways containing" text field in the Filter section of the left side bar, enter the KEGG id of the compound that you would like to exclude. Then click the "Apply" button.
  Either of these actions will hide all pathways containing the specified compound. Multiple compounds can be specified using either of these methods.


• Only include pathways containing specific compound(s): Similar to excluding pathways based on specific compounds, only displaying pathways containing specific compound(s) can be accomplished by right clicking a compound node or entering the KEGG id in the "Only include pathways containing" text field. Multiple compounds can be specified.


• Filter pathways by length: Pathways can be filted by the number of reactions in the pathway (length) by using the "Max path length" slider under the "Interactive Filter" section. Note: It is also possible to entering a maximum path length (# of reactions) in the "Exclude pathways longer than" text field under the Filter section. Click the "Apply" button to filter.


• Filter pathways by the number of conserved tracked carbon atoms: Pathways can be filtered by the number of conserved tracked carbon atoms by using the "Min carbons conserved" slider under "Interactive Filter" section. Note: It is also possible to entering a minimum number of tracked carbon atoms in the "Exclude pathways that conserve less than this number of carbons" text field under the Filter section. Click the "Apply" button to filter.


• Exclude pathways by ATPs produced/consumed: Pathways can be filtered by the net number of ATPs produced/consumed in the pathway using the "Min ATPs to produce" slider under the "Interactive Filter" section. A minimum number of ATPs produced can be specified by selecting a positive number, and a maximum number of ATPs consumed can be specified by selecting a negative number. Note: It is also possible to adjust this number in the "Exclude pathways that produce less than this number of ATPs" text field under the Filter section. Click the "Apply" button to filter.