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.
ModuLand: Cytoscape plug-in containing the Linkland and ProportionalHill methods
- Szalay-Bekő, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2012) ModuLand plug-in for Cytoscape: extensively overlapping network modules, community centrality and their use in biological networks. Bioinformatics, 28, 2202-2204,
- 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.
The current version is compatible with Cytoscape 3.0. The Cytoscape 2.8.X. compatible former version can be downloaded from here: http://linkgroup.hu/modules_bioinfo_download.php
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- Several example networks in standard GML network format and Cytoscape Session (CYS) format can be downloaded here.
- In the publication we also analyzed 2000 connected random subnetworks of the E. coli metabolic network. The random samples can be downloaded from here and the Python scripts creating the subnetworks are available here.
ModuLand method: full package containing the NodeLand, LinkLand, Perturland, Edgeweight, ProportionalHill, GradientHill and Totalhill methods
Changes of version 1.3 (June 2012)
- 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 firstname.lastname@example.org
- 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. Latest version: 1.3, released on 26.06.2012. (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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Successful applications of the ModuLand method
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