Network modules/communities

Summary: The ModuLand method-family

Background: Network communities help the functional organization and evolution of complex networks. However, the development of a method, which is both fast and accurate, provides modular overlaps and partitions of a heterogeneous network, has proven to be rather difficult.

Methodology/Principal Findings: Here we introduce the novel concept of ModuLand and its plug-in to the widely used Cytoscape progam, an integrative method family determining overlapping network modules as hills of an influence function-based, centrality-type community landscape, and including several widely used modularization methods as special cases. As various adaptations of the method family, we developed several algorithms, which provide an efficient analysis of weighted and directed networks, and (1) determine overlapping modules with high resolution; (2) uncover a detailed hierarchical network structure allowing an efficient, zoom-in analysis of large networks; (3) allow the determination of key network nodes and (4) help to predict network dynamics.

Conclusions/Significance: The concept opens a wide range of possibilities to develop new approaches and applications including network routing, classification, comparison and prediction.

Downloadable materials

Manuscript describing the ModuLand Cytoscape plug-in

Szalay-Bekő, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2011) ModuLand plug-in for Cytoscape: extensively overlapping modules, community centrality and their use in biological networks. Download it! http://arxiv.org/abs/1111.3033
Supplementary Material of the manuscript. Download it!
A detailed User Guide and Installation Instruction for the Cytoscape plug-in version of the optimal LinkLand version of the ModuLand method. Download it!
The ModuLand Cytoscape plug-in containing the optimal LinkLand version of the ModuLand method. Download and Register for newsletters!

Main manuscript describing the ModuLand method

Kovács, I.A., Palotai, R., Szalay-Bekő, M. and Csermely, P. (2010) Community landscapes: a novel, integrative approach for the determination of overlapping network modules. PLoS ONE 7, e12528, IF: 4.4 Download it!
www.arxiv.org/abs/0912.0161 Supporting web-site with all downloadable algorithms: www.linkgroup.hu/modules.php
Featured in the February 2011 issue of Science Signaling
Electronic Supplementary Material (ESM1) of the manuscript containing a detailed description of the ModuLand method including the pseudo-codes of all algorithms used, 14 Figures, 3 Tables (with 18 module definitions, 129 different modularization methods, 13 module comparision methods), a Supplementary Discussion and 384 references. Download it!
Revised Suppl. Table 2. We noted in the PLoS ONE paper that despite of our efforts - regretfully - a few errors occurred in the original Supplementary Table 2. Also, the original Supplementary Table 2 missed a few modularization methods. Thanking for the advice of our colleagues we have revised this Table, and placed the revised version here. Download it! In case of any further errors or missing methods feel free to contact us at csermely@eok.sote.hu
A detailed User Guide to use the original ModuLand program package containing several sub-methods of the ModuLand program family. Download it!
The ModuLand algorithm package described in the User Guide containing several sub-methods of the ModuLand program family and also including all network data used in the manuscript. (Please note that a Linux-based operating system is required for running the ModuLand programs included. Alternatively, a prebuilt VirtualBox Image is available for running the ModuLand programs on your computer.) Register and download!

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Other publications

You can find our previous network community-related publications here.
You can find the 2006 starting ideas of the ModuLand method as a patent application here.

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