NEXCADE: perturbation analysis for complex networks.

Gitanjali Yadav,Suresh Babu

doi:10.1371/journal.pone.0041827

Gitanjali Yadav, Suresh Babu

Open Access

https://doi.org/10.1371/journal.pone.0041827

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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.

Highlights

Complex dynamical systems govern the patterns and processes observed across all domains of life, ranging from molecular frameworks within our cells to large-scale ecological communities, even globally interlinked social associations, transportation networks and internet communication [1,2,3]
Based on our insights from an extensive analysis of the architecture of more than a hundred large publicly available real world networks and their responses under attack, we have developed NEXCADE, a program for simulation and analysis of perturbations in a complex system, and to monitor the altered system attributes at every step, in order to determine how associated perturbations are either generated or propagated from the previous event
NEXCADE has four major sections for the analysis of a given network, namely, (a) Visualization and Attributes (b) Single Perturbations (c) Grouped Perturbations and (d) Serial Perturbations, each of which enables users to carry out desired simulations and impact analysis

Summary

Introduction

Complex dynamical systems govern the patterns and processes observed across all domains of life, ranging from molecular frameworks within our cells to large-scale ecological communities, even globally interlinked social associations, transportation networks and internet communication [1,2,3]. The cascading or ‘targeted’ perturbation approach involves simulations of random or ordered primary extinctions based on a given node property such as the number of links or ‘degree’.

Results

Conclusion