HELP

Description

Drugs, Targets and Side Effects are shown as nodes in a network. The interactions between these different entities are schown by differently coloured edges. The network can be explored interactively by double-clicking on nodes directly in the network and by the use of a side-bar with context-sensitive options.

Create a new Network

There are three ways to create a new network:

1. Type Uniprot- and PubChem-Ids of molecules in the respective boxes, then click "Search". Multiple Ids of the same kind have to be seperated by a semicolon.
2. Upload a file containing an xml-representation of the network. The xml-representation must have been saved previously using the "Save network as xml" button.
3. Open the ATC-Tree, then select the classification you are interested in. This will load all drugs with this ATC-classification plus their interactions in the network.

Node Types

Three different kinds of nodes may be present in the network, distinguishable by their icons:

Drugs

Human targets (with/without known structure)

Nonhuman targets (with/without known structure)

Side Effects

Edge Types

Interactions between the different kinds of nodes are represented by edges that are coloured according to which kind of nodes they connect:

			Drug - Drug
			Drug - Human target
			Drug - Nonhuman target
			Drug - Side Effect
			Human target - Human target
			Human target - Human target (complex)
			Any selected interaction

Functions in the applet

Function	Command
Select a node or edge to get the context-sensitive sidebar displayed	Left click on the node or edge
Select multiple nodes	Press CTRL while clicking on the nodes
Drag a node around	Left click on a node and keep the mouse button pressed, then move the mouse around
Load a nodes interaction partners into the network	Double-click on the node
Delete a node from the network	Right click on the node while pressing SHIFT
Zoom the network	Use the zoom slider at top of the applet
Pan the network	Keep the right mouse button pressed and move the mouse around
Stop the drugs and targets from moving around	Left click on the "FIX NODES"-button. Click again to release them
Fix one node	Select the node, then press SPACE
Alter the edge lengths	Use the edge-length slider at top of the applet
Show/hide nodes	Click on the buttons "HIDE ..." to hide the respective kind of nodes
Change the appearance of the network	Use the three knobs in the upper left of the applet
Increase the speed of the visualisation	Klick on the "FASTER"-button

The context-sensitive sidebar

	Adds neighbour proteins, drugs or side-effects to the chosen entity. A maximum of 20 entities of each category can be added at once.
	Removes the chosen entity from the network. Note that deleting nodes from the network causes neighbors of the deleted node to float away. To circumvent this effect the user can simply hide and unhide nodes.
	By clicking on this option a new tab with the drug or target detail site respectively is open.
	Drugs with predicted similar action are loaded into the network. The drugs are fetched from SuperPred a group own drug-target prediction server.
	By clicking on this option all drugs belonging to the same ATC class as the chosen drug are highlighted in the network.
	To have a first insight into the
	For first insights of graph theoretical analysis basic average graph properties (Betweensess, Degree, Clustering Coefficient) for the current and the overall network are calculated.
	Displays a list of drugs which are known to cause the chosen side effect.
	Displays a list of drugs which share side-effects with the chosen drug, ranked by the number of shared side-effect.