Quickstart

Search for a Network

A powerful search engine is available from multiple places on the CBN portal for users to quickly locate networks of interest.

From the network viewer page, the advanced search is called by clicking on search networks

It opens a search box in a pop up window:

User may enter any text string to search within network name and description; the search also encompasses the list of nodes (genes/proteins) found within a network and pubmed identifier of literature references supporting edges. Search terms may range from broad biological concepts (e.g. macrophage) to specific molecular entities (e.g. IL-8).

As the user types within the text box, the search results are filtered out.

Search result. Example: search for "IL8"

All networks returned by the search are shown in the search results panel. User may scroll down to browse all results.

For each network returned, the icon of the network, name, version, and beginning of the network description are shown.

The user may then click on:

• "VIEW" to open the network in the network viewer environment
• "DETAILS" to open a pop up window with the full network description
• "EXPORT" to initiate the download of the network (see below)

View a Network

#1 Selecting A Model Initiates Display Within the Network Viewer Environment

Example: if we had clicked on "View" on the CV-IPN Plaque destabilization network when we looked for IL8, it would open the following window:

Note: by default, all node names are displayed.

#2 Display Network Detail

User may view network details by clicking on the network detail button.

#3 Hide/Display Nodes Names

To hide nodes names, click on "Toggle BEL":

#4 Change Network Layout

Default layout was prepared from the networks authors. The user may choose to:
Move nodes. To do so, deselect the "zoom" button. Each node can then be freely moved.

Visualize an automatic layout (force-directed layout) by clicking on "Force Diagram".

#5 "Nodes" Menu Provides Quick Access to Molecules or Processes of Interest

Select "NODE LIST" button to display a list of all nodes found in the network.

User may scroll down to see all edges or type in part of a node name to filter the list.

#6 Select Any Node From List to Highlight Associated Edge Connections

Click on any node to filter all edges connected to the node. The search tool may also be employed to quickly locate a node of interest.

#7 Select Any Edge From List to Highlight Associated Evidence

Then click on the context in the evidence list to display more information on the supporting evidence.

Evidence detail displays the name of the edge, the quotation from the scientific article that supports the relationship, the reference to the article, with a link to the abstract of the article in Pubmed, and the context annotation.

Download a Network

Networks may be downloaded as SIF and JSON Graph files from the search results, from the network carousel on the bottom of the home page, or from the network viewer by clicking on "EXPORT"

A pop-up window will open to ask the user where he/she wants to save the file.

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