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CompNet

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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.

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.

NetGestalt

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.

PaxtoolsR

Enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons web service for users of the R language. Features include the extraction, merging, and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons web service allowing users to query, extract, and retrieve data and integrate this data with local BioPAX datasets.

PaVESy / Pathway Visualization Editing System

Offers the possibility to map profiling data into established knowledge about biological pathways. PaVESy is a pathway database software that allows to process a whole data set profile in one step. This method integrates and compares numeric multi-parallel genomic, proteomic and metabolomic data with respect to publicly available pathway information and expert knowledge, which can be embedded by customized definitions of objects, attributes and interactions.

CySBML / Cytoscape Systems Biology Markup Language

Designed to work with Systems Biology Markup Language (SBML) in Cytoscape. CySBML includes an importer for BioModels to load SBML from standard repositories. Cytoscape has already been used in numerous applications for visualization and graphical network analyses, whereas the BioModels database collects and annotates structural and mathematical models in SBML format that provide insights into the dynamic behavior of biological networks. CySBML makes it possible to combine these two important system biological resources in a convenient and easy-to-use way with special focus on the semantic layer defining the models.

RadialTopologyViewer

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.

ProHits-viz

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.

STON / SBGN TO Neo4j

A graph-based tool to extend the existing infrastructure for storing and exploring biological pathways in Systems Biology Graphical Notation-Markup Language (SBGN-ML) format. STON can transform SBGN maps into a graph representation, thereby enabling: (i) efficient management and querying of networks, (ii) identification of subgraphs in networks, (iii) merging of existing pathways into larger networks. Ultimately, STON imports and translates metabolic signalling and gene regulatory pathways represented in the SBGN into a graph-oriented format compatible with the Neo4J graph database.

RedeR

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.

CyToStruct

A transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular viewers from the network's edges and nodes. CyToStruct enriches the network tools of Cytoscape by adding a layer of structural analysis, offering all capabilities implemented in molecular viewers. Given the coordinates of a molecular complex, our web server automatically generates all files needed to visualize the complex as a Cytoscape network with CyToStruct bridging to PyMOL, UCSF Chimera, VMD, and Jmol.

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.

BNOmics / Bayesian Network Omics

Infers and analyzes Bayesian Networks from omics datasets. BNOmics aims at comprehensive systems biology—type data exploration, including both generating new biological hypothesis and testing and validating the existing ones. Three features of BNOmics set it apart from comparable alternatives. Its high computational efficiency and scalability, flexibility and open nature of the source code and its immediate applicability to the large-scale datasets generated by the omics studies.

WebInterViewer

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.

PiiL / Pathway interactive visualization tooL

Allows direct comparison and testing specific hypotheses in model organisms for which pathway and expression network data exists. PiiL is an integrated DNAm and expression pathway browser. It was designed to explore and understand the effect of DNAm operating on individual CpG sites on overall expression patterns and transcriptional networks. It implements a multi-level paradigm, which allows examining global changes in expression, comparisons between multiple sample groupings, play-back of time series.

GraphWeb

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.

NaviCell

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).

LitPathExplorer

Allows exploration of literature-enriched pathway models. LitPathExplorer is a visual analytics tool that combines visual interactive analysis with state-of-heart text mining and semi-supervised learning methods for facilitating pathway reconstruction and revision. The software allows: (1) querying and exploration of pathway models; (2) integration of automatically extracted events from the literature; (3) computation and aggregation of multiple features for the calculation of confidence; and (4) close involvement of the domain expert in the analytical process.

NaviCom

A web application for visualization of multi-level omics data on top of biological network maps. NaviCom uses a large datasets from omics data resources to displaying them on a molecular network maps with optimized visualization settings. Navicom is a link between a resource of large-scale cancer omics data (cBioPortal) and a data visualization web service (NaviCell). Ultimately, this tool allows to create a comprehensive molecular portraits of cancer, identifying specific patterns in the data for a better disease subtypes classification.

VISUALGRAPHX

A web-based, interactive visualization tool for large-scale graphs. VisualGraphX aims to provide a universal graph visualization tool that empowers the users to efficiently explore the data for themselves at a large scale. It is available as a visualization plugin for the Galaxy platform, such that VisualGraphX can be integrated into custom analysis pipelines. Furthermore, the structure of VisualGraphX allows it to be extended for more specific use cases of graph visualization and its streaming design, where data is loaded and visualized on-demand, ensures its performance even for large scale graphs.

DyNet

A Cytoscape plug-in that visualizes differences among multiple networks. DyNet can be used for analysing how networks change over time or across multiple conditions (dynamic networks). DyNet utilizes Cytoscape’s own built-in network data structure, so there is no need for a specialized file format. Users can just import multiple networks separately as they would normally do and quickly use DyNet to highlight and identify differences that are present. In addition, DyNet also introduces a new method to highlight nodes that are most ‘rewired’. It takes into account actual changes in nodes’ connectivity (their connections to each neighbor separately). Therefore, this method can identify a node that is more strongly connected to different neighbors in different networks, even if its degree or the sum of its edge weights stays the same.

Medusa

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.

NetBioV / Network Biology Visualization

Allows the efficient visualization of large biological networks by emphasizing important aspects of biological information processing. NetBioV provides four principle types of layout styles: global, modular, information flow and hierarchical layouts. These can be used either separately or combined with each other, in a nested way. The organization of NetBioV is highly flexible enabling individualized network visualizations. Part of the functionality of NetBioV comes from its integration into R to borrow strength from existing package repositories and to ensure reproducible research by saving source code for the network visualization coordinates and parameters.

PathVisioRPC

An XML-RPC interface for the pathway analysis tool PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting results in several image formats in multiple programming environments. It supports the use of existing pathways from WikiPathways or pathways created using the RPC itself. It also enables automation of tasks performed using PathVisio, making it useful to PathVisio users performing repeated visualisation and analysis tasks.

DeDaL / Data-Driven Network Layouting

Allows constructing biological network layouts based on the data from molecular profiles imported as values of node attributes. DeDaL is a Cytoscape 3 app, which uses linear and non-linear algorithms of dimension reduction to produce data-driven network layouts based on multidimensional data (typically gene expression). DeDaL implements several data pre-processing and layout post-processing steps such as continuous morphing between two arbitrary network layouts and aligning one network layout with respect to another one by rotating and mirroring.

BioPAX translator

Allows users to create pathway diagrams using CellDesigner and save the data accurately in BioPAX format. The BioPAX translator is implemented as a CellDesigner plug-in, so that timely updates can be released. CellDesigner includes an extensible plug-in system that allows third-party software to register as plug-ins for additional functionality. The interface allows any plug-in to retrieve information such as model, compartments, components and relationships between components as well as the relationships between the components and the compartments.

BIANA / Biologic Interaction and Network Analysis

A tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties.

GraphiaPro

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.