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an interactive graphical browser for molecular interaction networks

•  Main Menu & Navigation
•  Node & Edge Data
•  Graph Display Options
•  Uploading Data

Graph Display Panel

The Graph Display Panel provides a network representation of available interaction data. It offers a number of interactive features for
manipulating the graph (see below) and communicates with Node & Edge Data. Additional aspects of the display layout can be
controlled using Main Menu & Navigation.

Graph layout:
N-Browse currently uses a dynamic spring layout to position nodes in the graph. This layout balances attractive and repulsive forces between nodes to find a local energy minimum for the layout.
Users are able to enable and use a weighted spring layout via the Edge Weights View (Weighted Formula View) under the Edit menu.

Moving graph elements
Holding down the mouse button and dragging the cursor can be used to move nodes or the entire graph:
 - Dragging with the cursor positioned over the background moves the entire graph.
 - Dragging with the cursor positioned over a node moves that node. 
Due to the dynamic spring layout, this will also cause the rest of the graph to follow suit (in test release version). If the node has been anchored (see below), it will remain pasted to the background in the new position.

Double-click on a node
Expands the graph around the selected node. All functional links to this node will be displayed.
All links between the new neighbors of this node and any nodes currently in the graph will also be displayed.
NOTE: To back up a step in the expansion of the graph, press the back arrow button in Main Menu & Navigation.

- Mousing over a node causes relevant information about that node (gene) to be displayed in Node & Edge Data.
- Mousing over an edge highlights the selected edge that could then be click on details of the edge type and numerical value, if any.

Multiple node select
Multiple nodes can be selected together for some operations by holding down the shift key while successively clicking on nodes to select them.

Tool Bar Icons (Single Left-click functionality)
N-Browse functionality based on one click. 

- centers graph back to the home position

- brings up dialog to color selected nodes in foreground and color background

and - enables/disables popup info for nodes and edges (disabled by default)

- increases size of nodes used in graph

- decreases size of nodes used in graph

- zooms into graph for closer details

- zooms out of graph for less details

- performs an additional layout calculation (default is spring)
note: will not force layout on anchored nodes

- performs an additional layout calculation (default is spring)
note: will force layout on anchored/unanchored nodes

- stops current layout calculation (default is spring)

and - enables/disables node dragging interaction mode (disabled by default)

- anchors selected nodes used in graph note: won't move during layout calculation unless forced

-unanchors selected nodes used in graph
node: nodes will be be affected by layout calculations

Right-click (Control-click for one-button mouse)
N-Browse displays a drop-down menu with several control options.

Control Options:

Color Node()
Gives ability to color node selected via color selection.

Hide Node ()
Hides node from view. These can be recovered by selecting "Unhide Nodes" menu option.

Anchor All Nodes ()
Pastes all nodes to the wallpaper. This prevents the nodes from moving around a when layout calculation is done.  When an expansion is done or a session file is loaded, the existing graph (prior to new nodes being added) become anchored.

Note: In test release, anchoring prevents nodes from moving when other nodes are dragged.

Unanchor All Nodes ()
Releases all nodes anchored from the wallpaper. This allows nodes to move around when a layout calculation is done.  A layout is done on new searches, additional layouts, on expansions (new nodes), and on nodes being dragged (test release).

Anchor Node ()
Pastes the node to the wallpaper. This prevents the node from moving around when other nodes are dragged or when the graph is expanded. See Anchor All Nodes for more informatio.

Unanchor Node()
Releases the anchor for the selected node, allowing it to float freely in space.  See UnanchorAll Nodes for more information.

Expand Node ()
Displays hidden neighbor nodes attached to selected node (see "Hide Node"). The number of hidden neighbors attached to each node, if any, is indicated in a small red tag on the edge of the node border.

Select Node Neighborhood()
Highlights neighboring one-hop nodes from selected node.

Select All Anchored Nodes()
Highlights all anchored nodes in the current graph.

Select All Unanchored Nodes()
Highlights all unanchored nodes in the current graph.

Select All Nodes()
Highlights all nodes in the current graph.

Unselect All Nodes()
Unhighlights all nodes in the current graph.

Invert Selection()
Highlights unselected nodes and unhighlights selected nodes.

Mouse/Keyboard Options:

Shift Left Click:
On node - node multi-select
On whitespace -centers the graph
Right Click:
Popup menu (used to be select node neighborhood)

Ctrl Left Click:
Same as right click - popup menu

Alt Left Click:
Select node neighborhood
Shift Right Click:
Hide Node
Ctrl Right Click:
Anchor Node (replacing current old Jnet menu)
Alt Right Click:
Unanchor Node
Ctrl Shift Right Click:
Unhide all nodes
Left Click:
On Node - exclusive node selection
On whitespace - clears node selection
On Jnet Text - old Jnet menu
Double Left Click:
On Node - node expansion
Left Click Drag:
On node - drags node (layout occurs if any nodes in graph not anchored)
On Whitespace - drags graph on screen
Alt Left Drag:
rotates graph left or right:
Shift Left Drag:
rubberband selection of nodes:
Middle Mouse Button Click: Zoom
Shift Right Drag:
Ctrl Shift Left Click Drag:
Rotates graph left or right
Middle Mouse Button Double Click:
Resets Graph