Summary: The extensively overlapping structure of network modules is an increasingly recognized feature of biological networks. Here we introduce a user-friendly implementation of our previous network module determination method, ModuLand , as a plug-in of the widely used Cytoscape program. We show the utility of this approach a.) to identify an extensively overlapping modular structure ; b.) to define a modular core and hierarchy allowing an easier functional annotation ; c.) to identify key nodes of high community centrality, modular overlap or bridgeness in protein structure, protein-protein interaction and metabolic networks. Availability and implementation: The ModuLand Cytoscape plug-in was written in C++, has a  JAVA-based graphical interface  , can be installed as a single plug-in and can run on Windows, Linux, or Mac OS.  The plug-in and its user guide can be downloaded  from: URL
Summary: The ModuLand plug-in provides Cytoscape users an algorithm determining a.) extensively overlapping network modules ; b.) several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer ; c.) module cores predicting the function of the whole module; and d.) key nodes bridging two or multiple modules in complex networks. The plug-in was written in C++, has a detailed JAVA-based graphical interface with various colouring options , can be installed as a single file and can run on Windows, Linux, or Mac OS. We demonstrate its use on protein structure and metabolic networks. Availability: The plug-in and its user guide can be downloaded freely from: URL
R
extensively overlapping structure of network modules is an increasingly recognized feature of biological networks. Here we introduce a user-friendly implementation of our previous network module determination method, ModuLand , as a
ModuLand
R
of the widely used Cytoscape program. We show the utility of this approach
provides Cytoscape users an algorithm determining
R
to identify an extensively overlapping modular structure
extensively overlapping network modules
R
to define a modular core and hierarchy allowing an easier functional annotation
several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer
R
to identify key nodes of high community centrality, modular overlap or bridgeness in protein structure, protein-protein interaction and metabolic networks. Availability and implementation: The ModuLand Cytoscape
module cores predicting the function of the whole module; and d.) key nodes bridging two or multiple modules in complex networks. The
A
detailed
A
with various colouring options
R
plug-in
file
A
We demonstrate its use on protein structure and metabolic networks. Availability:
A
freely