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Cytoscape
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Review

Cytoscape

Overview
Synopsis

Cytoscape software visualizes complex networks and integrates them with any attribute data. It is an open source software which visualizes molecular interactions and biological pathways integrating them with annotations.

Category

Data Visualization Software Open Source

Features

•Supports Many Standards
•Public Database Clients
•Interoperability
•Session File
•Layout
•mage Export
•VizMapper
•Filter
•Search
•Browsing
•Find Modules/ Clusters
•App Manager and App Store
•Multilingual
•Export to Web

License

Open Source

Price

Free

Pricing

Subscription

Free Trial

Available

Users Size

Small (<50 employees), Medium (50 to 1000 employees), Enterprise (>1001 employees)

Company

Cytoscape

What is best?

•Supports Many Standards
•Public Database Clients
•Interoperability
•Session File
•Layout
•mage Export
•VizMapper

PAT Rating™ ( Beta)
Editor Rating
Aggregated User Rating
Rate Here
Ease of use
8.0
8.7
Features & Functionality
7.9
8.4
Advanced Features
8.1
8.0
Integration
8.1
8.4
Performance
7.9
8.7
Customer Support
8.0
8.9
Implementation
8.0
Renew & Recommend
8.0
Bottom Line

Cytoscape is an open source software which visualizes molecular interaction networks and biological pathways and integrates them with annotations, gene expression profiles, and other state data.

8.0
Editor Rating
8.4
Aggregated User Rating
3 ratings
You have rated this

Cytoscape software visualizes complex networks and integrates them with any attribute data. It is an open source software which visualizes molecular interactions and biological pathways integrating them with annotations, profiles of gene expressions and other types of state data. Originally designed for biological research, the software is now a general platform for visualization and complex network analysis. The software contains features for data integration, visualization, and analysis with other applications as additional features. The Apps are designed for molecular and network profile analyses, scripting, additional file format support and database connections.

Cytoscape 3 is the mainstream for Cytoscape software with modular architecture designed for long term maintainability. Cytoscape 3 is a java application for the desktop for visualization and large network analysis. It has a user interface with advanced visualization functions, command-line distributions, multiple engine support and RESTful API. The software supports many standard networks and file formats. The software allows a user to import data enabling the loading and saving of arbitrary attributes on edges, nodes, and networks.Cytoscape directly connects to external databases and imports annotation data and networks acting as a web service client. Cytoscape software also loads files and texts for other bioinformatics using networks generated by igraph or Bioconductor.

The Cytoscape session feature available in the software saves information in a click. It contains settings, visualizations and data files. It contains logarithms including cyclic, edge weight, force directed and yfiles organic layouts. The software exports data as publishable quality images. It is also possible to modify vector images using the available applications such as adobe illustrator. The software allows the filter of nodes based on current data. Filtering results create new networks. There are visual styles in the software features used for customizing network data display. One can also find modules and clusters by screening networks against gene expression data. Most Cytoscape's features allow other languages using two-byte characters including eastern Asian languages excluding English.

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1 Reviews
  • Evan
    October 13, 2017 at 3:26 pm

    Network Data Integration, Analysis, and Visualization in a Box.

    Company size

    Medium (50 to 1000)

    User Role

    Executive

    User Industry

    Construction

    Rating
    Ease of use8.7

    Features & Functionality8.4

    Project and integrate global datasets and functional annotations. Establish powerful visual mappings across these data. Perform advanced analysis and modeling using Cytoscape Apps.

    Advanced Features8

    Integration8.9

    Training 8.9

    Customer Support8.9

    Renew & Recommend8

    ADDITIONAL INFORMATION
    Cytoscape is 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. Cytoscape can directly connect to the external public databases and imports network and annotation data.

Ease of use
Features & Functionality
Advanced Features
Integration
Performance
Customer Support
Implementation
Renew & Recommend

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