Network visualization software tools | Shotgun metagenomic sequencing data analysis
Networks are becoming increasingly important to understand the relationships between genotype and phenotype, specifically in the context of disease. Consequently, the demand for efficient network visualization and analysis tools, which can interoperate with modern data analysis environments, such as the web, is increasing in parallel.
Integrates workflow technology and in-built access to bioinformatics resources including remote data warehouses and tools. Galaxy permits users without programming skills to conduct computational analysis through the Web. It builds a succession of tools to perform multistep studies and is able to conserve the complete provenance of each analysis step. This platform offers drag and drop functionalities to ease the construction of workflows.
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.
Records common knowledge represented in biological pathways. WikiPathways is a collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. It was developed to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community. This online database is improved by continuous data curation.
Creates and manipulates graphs. Igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. It is intended to be as powerful and fast as possible to enable the analysis of large graphs. This package can be programmed in R, in C/C++ and in Python. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
A system to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.
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.
Allows analysis of biological networks. VisANT is a workbench for the integrative analysis of biological networks, which aims assist network analysis by integrating biological knowledge from different sources or layers of complexity. The software provides exploratory navigation to walk through the interactions and metagraph capability for multi-scale visualization with integrated context information.