NEXCADE

NEXCADE is a program for simulating perturbations on a given Network

NETWORK:
Any complex system that can be conceptualized in the form of a web, and represented as interconnected matrices of interactions.

NODE:
Nodes of the network may represent genes, proteins, biochemical pathways, taxonomic species or any interactor of interest.

EDGE:
Edges of a network represent relationships between the nodes, which may be co-expression similarities, molecular interactions, taxnomic relationships, social connections etc

PERTURBATION:
A perturbation represents the destruction of selected Nodes and/or Edges in the network. In the former case, the destruction may represent removal/deletion/extinction of an interactor. The latter perturbation represents the elimination of the relationship or interaction between two nodes of the network.

NEXCADE allows users to simulate single, multiple, grouped or consecutive/cascading perturbations to their network of interest, as described here

CONSEQUENCES:
At every instance of a perturbation, a change occurs in the overall state of a system, derived from linkages that may be latent and superficially unrecognized. Once set in motion, however, such a change may become explosive and in extreme cases, lead to irreversible collapse through a cascade of detrimental effects. For example, the extinction of an important species in an ecosystem may sometimes trigger an avalanche of secondary extinctions, of species that were dependent on the lost organism.

NEXCADE allows users to visualize and analyse the consequence of a specific perturbation in several ways, as described here

Simulation of node 'Extinction' is analogous to a network perturbation that may have system-wide (systemic) consequences. In qualitative terms, a perturbation may represent a synthetic lethal mutation, a biochemical event, or a species extinction.

FOR EXAMPLE:

In a protein-protein interaction network, node-extinction can be equated with the deletion of a given protein from the network.

In a genetic interaction network, the simulation reveals the effect of knocking-out a specific regulator.

In an expression network, node removal would signify a mutation blocking the induction of a given gene.

In an ecological network, the server simulates the extinction of a given species on the community being studied.

In a social network, a perturbation could mean the mortality of an individual.

FOR THE NEXT TUTORIAL ON NEXCADE BASICS, PLEASE CLICK HERE