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This project implements a Cytoscape plugin for viewing and manipulating pathway maps for metabolic models created by the Model SEED (http://www.theseed.org/models). See the quot;Filesquot; area for README. See Project Homepage for Tutorial.
The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations.
NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues.
GraphML Reader/Writer for CytoscapeGraphmlreader is a Cytoscape plugin for reading and writing basic GraphML file. Currently, this plugin is still in early stage of development and not supported the following features: Hyperedges Nested Networks Release note
This project consists of a database and Cytoscape plugin called the Ageing Cross-Species Interactome Database (ACID), which allows the identification of pathways between a source and target gene using integrated probabilistic functional integrated networks and gene expression data. The plugin is user-friendly and freely available. ACID is licensed under GNU General Public Licence v3 and is open-source. Download and installation instructions are available from the Web site: http://www.students.nc
The PerturbationAnalyzer is an open source Java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect
The basic idea behind the project is to distribute networks for visualization. There are few sites online that display networks with meta information on the screen. Those sites are mostly static and do not have the flexibility to adjust the network layout. The aim of the phpXgmml package is to provide you with the possibility to export networks as extended XGMML files and load those into visualization tools like Cytoscape to adjust networks to your likings. phpxgmml is focused on PHP5 using Cyto