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An open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.
Summarizes and displays scored quantitative protein interaction data in intuitive ways. ProHits-viz consists of four data analysis and image generation tools complemented by interactive viewers. The analysis tools can (i) cluster baits and prey for dot plot images, (ii) perform correlation analysis, (iii) calculate prey specificity scores and, (iv) generate detailed bait–bait comparisons. This method enables visualization of the results from the dot plot and correlation tools directly in the browser.
A web application for integrating multidimensional omics data over biological networks. NetGestalt exploits the inherent hierarchical modular architecture of biological networks to achieve high scalability. In contrast with typical network visualization tools, NetGestalt allows multiscale representation and navigation of the data, and it adjusts graphical presentations to the level of detail appropriate to a particular scale. It also allows simultaneous visualization of different types of data within the same framework to facilitate data integration.
An open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community.
A powerful tool for the visualization and analysis of network graphs. Network-based approaches are becoming increasingly popular for the analysis of complex systems of interaction and high dimensional data. Networks can be produced from a wide variety of relationships between entities. In biology this includes the interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, etc. GraphiaPro has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not exclusively, from biological data.
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Allows simultaneous visualization and comparison of multiple networks. In addition to computing generic graph properties for individual networks, CompNet allows multigraph comparisons and similarity based grouping of networks. It also allows visual identification and selection of sub-graphs/communities of interest, enabling a general user to work with and compare between sufficiently complex and large networks. CompNet is a valuable tool for biologists and other researchers working in the field of visual data mining.
A java standalone application for visualization and clustering analysis of biological networks in 2D. Medusa is highly interactive and it supports weighted and multi-edged graphs where each edge between two bioentities can represent a different biological concept. Comparing to previous versions, it is currently enriched with a variety of layout and clustering methods for more intuitive visualizations. It is easy to integrate with web application since it is offered as an applet.
Provides a comprehensive and entirely framework to read, write and manipulate R code mixed to a Java data structure. RedeR is designed for the representation of nested and hierarchical biological networks. Its architecture allows the creation of R-based plugins with minimum effort, potentially extending the existing R packages to different communities of users interested in studying biological networks. RedeR also implements a framework for network comparison and module representation by introducing a hierarchy of ‘containers’ in which many networks and their connections can be visualized at the same time.
ChiBE / Chisio BioPAX Editor
Allows users to tap into the detailed pathway information corpus for genomic data analysis. This would not be possible without its three key features: process views, specialized graph queries, and integration with genomic data repositories. Process views show the mechanism of events, bringing causality and context to the gene interactions. Graph queries enable users to define context specific boundaries for pathways. Automated mapping from genomic data repositories onto pathways streamlines the analysis, eliminating manual formatting steps.
Allows the visual investigation of potential biological effects of alternative splicing. DomainGraph is a plugin for Cytoscape that directly loads and analyzes AltAnalyze alternative exon statistics, without requiring prior knowledge of genes or pathways potentially affected by alternative splicing. The software annotates statistically enriched probe sets with gene and pathway information. The visual network analytics provided can be used to investigate the potential biological implications of alternative splicing events and related mechanisms in the context of molecular interactions and binding sites.
Allows for biological network analysis and module discovery. GraphWeb provides methods to: (i) integrate heterogeneous and multispecies data for constructing directed and undirected, weighted and unweighted networks; (ii) discover network modules using a variety of algorithms and topological filters and (iii) interpret modules using functional knowledge of the Gene Ontology (GO) and pathways, as well as regulatory features such as binding motifs and microRNA targets. GraphWeb is designed to analyse individual or multiple merged networks, search for conserved features across multiple species, mine large biological networks for smaller modules, discover novel candidates and connections for known pathways and compare results of high-throughput datasets. The GraphWeb is freely available online.
A web server designed to create colourful, visually pleasing and biologically accurate pathway diagrams that are both machine-readable and interactive. As a web server, PathWhiz is accessible from almost any place and compatible with essentially any operating system. It also houses a public library of pathways and pathway components that can be easily viewed and expanded upon by its users. PathWhiz allows users to readily generate biologically complex pathways by using a specially designed drawing palette to quickly render metabolites (including automated structure generation), proteins (including quaternary structures, covalent modifications and cofactors), nucleic acids, membranes, subcellular structures, cells, tissues and organs.
A tool for network-based visualization of ‘omics’ data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R).
Analyzes the interactions from any system. WebInterViewer is a web-based application program that produces a molecular interaction network of good quality without computing force between every pair of nodes. It can visualize molecular interaction networks as layered graphs consisting of three layers: domain, function and molecule layers. WebInterViewer provides two ways of comparing multiple molecular interaction networks: (i) to find a subnetwork shared by all networks being compared, the other to find a subnetwork shared by some of the networks, by coloring the networks.
A versatile web server for interactive network analysis and visualization. StemCellNet rapidly generates focused networks based on a large collection of physical and regulatory interactions identified in human and murine stem cells. The StemCellNet web-interface has various easy-to-use tools for selection and prioritization of network components, as well as for integration of expression data provided by the user. As a unique feature, the networks generated can be screened against a compendium of stemness-associated genes. StemCellNet can also indicate novel candidate genes by evaluating their connectivity patterns. Finally, an optional dataset of generic interactions, which provides large coverage of the human and mouse proteome, extends the versatility of StemCellNet to other biomedical research areas in which stem cells play important roles, such as in degenerative diseases or cancer.
CAFE / aCcelerated Alignment-FrEe sequence analysis
Calculates 28 alignment free dissimilarity measures. CAFE allows visualization of pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. It allows the user to study the relationships among genomes and metagenomes. The tool is based on a k-mer alignment-free method and contains 10 conventional measures based on k-mer counts. It also integrates 15 measures based on presence/absence of k-mers.
Performs a graphical visualization of a bait protein interactome derived from a co-immunoprecipitation experiment. RadialTopologyViewer presents the bait as center of the interactome and all interactions identified are positioned in relative proximity to the central bait protein. In contrast to a standard network representation, the length of the edge between the central bait and the interactor can be fixed such that it reflects a property between the bait and the interactor. For example the user can choose to display the likelihood of interaction between the bait and the interactor as a function of the edge length. Moreover, interacting proteins can be grouped together in radial spokes according to a classifier like common GO term.
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Serves for the analysis of human data. 3Omics simplifies the data analysis by combining the advantages and operations of several existing systems and packages into a single platform. It accepts multiple experimental conditions or time-dependent transcriptomics data, proteomics data or metabolomics data. Users can perform correlation analysis, coexpression profiling, phenotype mapping, pathway enrichment analysis and Gene Ontology (GO) enrichment analysis.
A free open-source pathway analysis and drawing software. PathVisio allows you to draw, edit and analyse biological pathways. You can visualize your own experimental data on the pathways and find relevant pathways that are over-represented in your data set. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins. Plugins are available for pathway building, pathway analysis, import/export functionality, data visualization or data integration. Plugins may be developed by anyone by using the PathVisio Plugin API.
Cytoscape Web
Allows network visualization. Cytoscape Web can be customized and incorporated into any web site. It allows the client application to define a network of nodes and edges and customize their attributes. The tool permits to dynamically change node and edge visual styles, using any of the following methods: specifying default visual properties for all elements; mapping node and edge attributes to visual styles; and overriding default or mapped styles by setting a bypass style.
MIM notation / Molecular Interaction Maps notation
Provides a list of convention for annotating and organize relationships in bioregulatory systems. MIM notation describes the relationships between multiple entities by using interactions glyphs, a controlled vocabulary and typographical convention. The system is able to display complex set of regulatory network interconnections or to capture different cell types and cell states. It also allows the specification of known molecular data as well as the addition of contingencies.
VANTED / Visualization and Analysis of Networks containing Experimental Data
A framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconstruction, data visualization, integration of various data types, network simulation to data exploration combined with a manifold support of systems biology standards for visualization and data exchange. The offered set of functionalities is instantiated by combining several tasks in order to enable users to view and explore a comprehensive dataset from different perspectives.
Provides pathway based data integration and visualization. Pathview maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
NAViGaTOR / Network Analysis, Visualization, & Graphing TORonto
A powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. Publication-quality images can be rendered through SVG graphics export. NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture.
Provides class-guided network visualization in Cytoscape. GOlorize uses Gene Ontology (GO) categories or other additional class information to direct the network graph layout process and to emphasize the biological function of the nodes. It can be used in conjunction with the BiNGO plug-in, an efficient tool to find the GO categories that are overrepresented in a selected part of the network. GOlorize first highlights the nodes that belong to the same class using color-coding and then constructs an enhanced visualization of the network using a class-directed layout algorithm.
Provides a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. LibSBGN makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. LibSBGN will help to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.
Provides several integrative and interactive visualization and analysis tools for protein-protein interaction (PPI) networks. Unlike VisANT, we use a cluster-centric top-down approach. Given a PPI network and a predefined clustering of its proteins, GenePro first provides a low-resolution view by displaying the protein clusters as individual nodes that are interconnected through interacting or shared proteins. For higher resolution views, individual clusters can be expanded to allow for more detailed analyses of clusters in terms of their component proteins and their interactions in the context of the full PPI network.
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