IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0041827.html
   My bibliography  Save this article

NEXCADE: Perturbation Analysis for Complex Networks

Author

Listed:
  • Gitanjali Yadav
  • Suresh Babu

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.

Suggested Citation

  • Gitanjali Yadav & Suresh Babu, 2012. "NEXCADE: Perturbation Analysis for Complex Networks," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-11, August.
    • Handle: RePEc:plo:pone00:0041827
    DOI: 10.1371/journal.pone.0041827
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041827
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0041827&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0041827?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. H. Jeong & S. P. Mason & A.-L. Barabási & Z. N. Oltvai, 2001. "Lethality and centrality in protein networks," Nature, Nature, vol. 411(6833), pages 41-42, May.
    2. Réka Albert & Hawoong Jeong & Albert-László Barabási, 2000. "Error and attack tolerance of complex networks," Nature, Nature, vol. 406(6794), pages 378-382, July.
    3. Roger Guimerà & Luís A. Nunes Amaral, 2005. "Functional cartography of complex metabolic networks," Nature, Nature, vol. 433(7028), pages 895-900, February.
    4. Enrico L. Rezende & Jessica E. Lavabre & Paulo R. Guimarães & Pedro Jordano & Jordi Bascompte, 2007. "Non-random coextinctions in phylogenetically structured mutualistic networks," Nature, Nature, vol. 448(7156), pages 925-928, August.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Miquel Duran-Frigola & Lydia Siragusa & Eytan Ruppin & Xavier Barril & Gabriele Cruciani & Patrick Aloy, 2017. "Detecting similar binding pockets to enable systems polypharmacology," PLOS Computational Biology, Public Library of Science, vol. 13(6), pages 1-18, June.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Laurienti, Paul J. & Joyce, Karen E. & Telesford, Qawi K. & Burdette, Jonathan H. & Hayasaka, Satoru, 2011. "Universal fractal scaling of self-organized networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(20), pages 3608-3613.
    2. Gao, Jianbo & Hu, Jing, 2014. "Financial crisis, Omori's law, and negative entropy flow," International Review of Financial Analysis, Elsevier, vol. 33(C), pages 79-86.
    3. Nicholas S. Vonortas & Koichiro Okamura, 2013. "Network structure and robustness: lessons for research programme design," Economics of Innovation and New Technology, Taylor & Francis Journals, vol. 22(4), pages 392-411, June.
    4. Gong, Pulin & van Leeuwen, Cees, 2003. "Emergence of scale-free network with chaotic units," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 321(3), pages 679-688.
    5. Xionglei He & Jianzhi Zhang, 2006. "Why Do Hubs Tend to Be Essential in Protein Networks?," PLOS Genetics, Public Library of Science, vol. 2(6), pages 1-9, June.
    6. Jordán, Ferenc, 2022. "The network perspective: Vertical connections linking organizational levels," Ecological Modelling, Elsevier, vol. 473(C).
    7. P.B., Divya & Lekha, Divya Sindhu & Johnson, T.P. & Balakrishnan, Kannan, 2022. "Vulnerability of link-weighted complex networks in central attacks and fallback strategy," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 590(C).
    8. Hou, Bonan & Yao, Yiping & Liao, Dongsheng, 2012. "Identifying all-around nodes for spreading dynamics in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(15), pages 4012-4017.
    9. Demetrius, Lloyd & Manke, Thomas, 2005. "Robustness and network evolution—an entropic principle," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 346(3), pages 682-696.
    10. Dan Braha & Yaneer Bar-Yam, 2004. "Information Flow Structure in Large-Scale Product Development Organizational Networks," Industrial Organization 0407012, University Library of Munich, Germany.
    11. Peter Langfelder & Paul S Mischel & Steve Horvath, 2013. "When Is Hub Gene Selection Better than Standard Meta-Analysis?," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-16, April.
    12. Milena Oehlers & Benjamin Fabian, 2021. "Graph Metrics for Network Robustness—A Survey," Mathematics, MDPI, vol. 9(8), pages 1-48, April.
    13. Yong He & Jinhui Wang & Liang Wang & Zhang J Chen & Chaogan Yan & Hong Yang & Hehan Tang & Chaozhe Zhu & Qiyong Gong & Yufeng Zang & Alan C Evans, 2009. "Uncovering Intrinsic Modular Organization of Spontaneous Brain Activity in Humans," PLOS ONE, Public Library of Science, vol. 4(4), pages 1-18, April.
    14. Serra, Roberto & Villani, Marco & Agostini, Luca, 2004. "On the dynamics of random Boolean networks with scale-free outgoing connections," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 339(3), pages 665-673.
    15. Takeshi Hase & Yoshihito Niimura & Tsuguchika Kaminuma & Hiroshi Tanaka, 2008. "Non-Uniform Survival Rate of Heterodimerization Links in the Evolution of the Yeast Protein-Protein Interaction Network," PLOS ONE, Public Library of Science, vol. 3(2), pages 1-7, February.
    16. Xia Cao & Chuanyun Li & Wei Chen & Jinqiu Li & Chaoran Lin, 2020. "Research on the invulnerability and optimization of the technical cooperation innovation network based on the patent perspective—A case study of new energy vehicles," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-19, September.
    17. Marcus Engsig & Alejandro Tejedor & Yamir Moreno & Efi Foufoula-Georgiou & Chaouki Kasmi, 2024. "DomiRank Centrality reveals structural fragility of complex networks via node dominance," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    18. Fabio Caccioli & J. Doyne Farmer & Nick Foti & Daniel Rockmore, 2013. "How interbank lending amplifies overlapping portfolio contagion: A case study of the Austrian banking network," Papers 1306.3704, arXiv.org.
    19. N. Foti & S. Pauls & Daniel N. Rockmore, 2011. "Stability of the World Trade Web over Time - An Extinction Analysis," Papers 1104.4380, arXiv.org, revised May 2011.
    20. Önder Kartal & Oliver Ebenhöh, 2009. "Ground State Robustness as an Evolutionary Design Principle in Signaling Networks," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-8, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0041827. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.