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STEP WISE ASSISTANCE TUTORIAL
DATA ANALYSIS: SECTION II: SIMULATION OF SINGLE PERTURBATION
The second section of the Main Results Window shown below, allows users to carry out single perturbations on the network in terms of destruction of specific nodes and edges.
[The format of this page is the same for both 'Your Web' and 'Browse Webs' sections of NEXCADE.]
As seen above, the second section allows users to perturb the node (depicted as protein in this example; sub-section A below) or an edge (see sub-section B below) of interest.
A: SPECIFIC NODE PERTURBATION
One can use the drop down menu to select any node in the network.
On clicking the 'simulate' button for selected node loss, the following page is returned:
As shown above, the program enables monitoring the status of network BEFORE (Section IIA) and AFTER (Section IIB) perturbation.
BEFORE NODE PERTURBATION : In this section, users can view all interactions and attributes of the node specific for pertubation
Clicking on the first link in Section IIA will return a list of interactions as shown below:
Clicking on the second link in Section IIA will return the various graph based attributes of the targeted node as follows:
AFTER NODE PERTURBATION : In this section, users can visualize the resulting subnetwork after perturbation and guage the network response in terms of propagating disturbances, if any, or changes in topology and connectivity, and monitor the altered node and network level attributes.
In addition, users can view/save all interactions and attributes of the node specific for pertubation
Clicking on the first link in Section IIB will return a page similar to the 'Network Visualization' (second figure in the Visualization tutorial).
From this page, users can save/download/compare important attributes of the reduced subnetwork, as well as the node level properties of each remaining node of the subnetwork.
The second line in Section IIB provides information on any associated co-extinctions or disturbances that may have propagated from the induced perturbation. In case any secondary damage has occured, as in this case, where five associated extinctions have taken place, users can view/save/download the list of affected nodes by clicking on the fourth link in this section, which will result in the following (if applicable):
Clicking on the third link in Section IIB will return a list of interactions remaining in the graph after perturbation.
[Note that this list can be used as input data for nexcade if users wish to perform additional perturbations on the reduced subnetwork.]
B: SPECIFIC EDGE PERTURBATION
As described earlier, one can use the drop down menu to select any node in the network, whose edge has to be targeted.
On clicking the 'simulate' button for selected edge loss, the following page is returned:
As seen above, the selected node has a total of ten edges in the network and any of these ten can be selected for perturbation using the drop down menu in Section IIB of this page. Clicking on the 'Remove Now' button will simulate edge perturbation and return the following:
As seen above, users can visualize the changes in several attributes of the reduced subnetwork after targeted edge perturbation. In this example, the number of vertices decreases by one after perturbation, suggesting an associated co-extinction. In such a case, the third and fourth links on this page provide further details about the propagated disturbance.
NEXCADE allows users to visualize the reduced sub-network by clicking the third link on this page which will return a page similar to the 'Network Visualization' (second figure in the Visualization tutorial).
From this page, users can save/download/compare important attributes of the reduced subnetwork, as well as the node level properties of each remaining node of the subnetwork.
This completes the tutorial on single network perturbation using NEXCADE.
For the third section that describes 'Grouped Perturbations', click here.
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