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PLoS One. 2012;7(8):e41827. doi: 10.1371/journal.pone.0041827. Epub 2012 Aug 3.

NEXCADE: perturbation analysis for complex networks.

Author information

1
Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India. gy@nipgr.res.in

Abstract

Recent advances in network theory have led to considerable progress in our understanding of complex real world systems and their behavior in response to external threats or fluctuations. Much of this research has been invigorated by demonstration of the 'robust, yet fragile' nature of cellular and large-scale systems transcending biology, sociology, and ecology, through application of the network theory to diverse interactions observed in nature such as plant-pollinator, seed-dispersal agent and host-parasite relationships. In this work, we report the development of NEXCADE, an automated and interactive program for inducing disturbances into complex systems defined by networks, focusing on the changes in global network topology and connectivity as a function of the perturbation. NEXCADE uses a graph theoretical approach to simulate perturbations in a user-defined manner, singly, in clusters, or sequentially. To demonstrate the promise it holds for broader adoption by the research community, we provide pre-simulated examples from diverse real-world networks including eukaryotic protein-protein interaction networks, fungal biochemical networks, a variety of ecological food webs in nature as well as social networks. NEXCADE not only enables network visualization at every step of the targeted attacks, but also allows risk assessment, i.e. identification of nodes critical for the robustness of the system of interest, in order to devise and implement context-based strategies for restructuring a network, or to achieve resilience against link or node failures. Source code and license for the software, designed to work on a Linux-based operating system (OS) can be downloaded at http://www.nipgr.res.in/nexcade_download.html. In addition, we have developed NEXCADE as an OS-independent online web server freely available to the scientific community without any login requirement at http://www.nipgr.res.in/nexcade.html.

PMID:
22870252
PMCID:
PMC3411682
DOI:
10.1371/journal.pone.0041827
[Indexed for MEDLINE]
Free PMC Article

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