Name: Overview of the Cytoscape Ecosystem
Uploaded: 2022-02-02T22:10:09.000Z
Duration: 56 min 33 s
Description: Overview of the Cytoscape Ecosystem

Help Desk

Web and Video Conferencing

Customer Support

Augmented Reality Development

Batch Management Software

Software Configuration Management

Development

Business Intelligence (BI)

Collaboration

Data Discovery and Visualization

Digital Rights Management (DRM)

Document Management

Dropshipping

Electronic Signature

Operational Analytics

Enterprise

Accounting

Trust Management

Finance and Accounting

Applicant Tracking

Corporate Learning Management

Corporate Volunteering

HR Management

Payroll

Recruitment Agency

Relocation

Talent Intelligence

Talent Management

Workforce Analytics

Workforce Management

eLearning Content

Human Resources

3D Printing

AI Governance

Application Lifecycle Management (ALM)

Cloud Storage

Consulting and Advisory Services

Content Delivery Networks (CDN)

Data Fabric

Data Recovery Service

Fraud Detection

Hadoop-Related

Integration Platform as a Service (iPaaS)

Internet Performance Monitoring

Managed File Transfer (MFT)

Network Performance Monitoring

Office Migration and Repair

Robotic Process Automation (RPA)

System Monitoring

Zero Trust Security Solutions

Information Technology

A/B Testing

Ad Serving & Retargeting

All-in-One Marketing

Audience Engagement

Blogging

Competitive Intelligence

Content Management

Email Marketing

Local Marketing

Marketing Automation

Social Media Management

Survey & Forms Building

Text to Speech

Web Analytics

Wholesale Marketplace

Marketing

Job Site Management

Project Management

Waste Management

Writing and Proofreading Tools

Professional Services

Customer Relationship Management (CRM)

Sales

Cloud Access Security Brokers

User and Entity Behavior Analytics (UEBA)

Security

Architecture

Camp Management

Chargeback Management

Dental

Digital Forensics

Nonprofit CRM

Plagiarism Checker

Vertical-Specific

Find top rated software and services based on in-depth reviews from verified users. 400+ software categories including PaaS, NoSQL, BI, HR, and more.

Databox

Tableau Public

Tableau

Grafana

Grafana Labs

Kibana

Elastic

Looker Studio

Google

Klipfolio Klips

Klipfolio

Sisense for Cloud Data Teams

Sisense Ltd

Chartio (discontinued)

Atlassian

Wolfram Mathematica

Wolfram

Conga Grid

Conga

Cytoscape is a software solution developed by the Cytoscape Consortium, designed for network data integration, analysis, and visualization. It caters to businesses of various sizes, from small companies to large research institutions. Professionals in industries such as biology, genetics, bioinformatics, systems biology, proteomics research, and social network analysis rely on Cytoscape for their network analysis needs.

## Key Features

**Network Data Integration**: Cytoscape enables users to integrate and visualize complex networks, including molecular and genetic interaction data sets, in various standard formats. Users can load and project global datasets and functional annotations onto their networks. The software supports the establishment of visual mappings across different types of attribute data.

**Analysis and Modeling**: Cytoscape provides advanced analysis and modeling capabilities through its Apps. Users can perform various analyses, such as network clustering, pathway enrichment, and network motif detection. The platform supports the creation and execution of custom analysis workflows.

**Visualization**: Cytoscape offers powerful visualization tools for exploring and analyzing network data. Users can create customizable visualizations of their networks, including options for node and edge colors, shapes, and sizes. The software supports the integration of external data sources to enhance visualizations.

**App Ecosystem**: Cytoscape has a variety of Apps available for different problem domains, including bioinformatics, social network analysis, and semantic web. Users can extend the functionality of Cytoscape by installing and using these Apps. The platform provides a marketplace for discovering and downloading new Apps.

**Data Import and Export**: Cytoscape allows users to import and export network and attribute data in various formats, including standard file formats and web services. The software supports the integration of external data sources, such as molecular interaction databases and pathway datasets. Users can easily share their network data with others by exporting it in a compatible format.

**Community and Support**: Cytoscape has an active and supportive community of users and developers. Users can access tutorials, documentation, and sample visualizations to learn and explore the capabilities of the software. The platform offers support through forums and mailing lists, where users can ask questions and receive assistance from the community.

**Automation and Integration**: Cytoscape provides automation capabilities through its CyREST API, allowing users to leverage command-line tools, R, and Python libraries. Users can automate their analysis workflows and integrate Cytoscape with other software or data analysis pipelines. The platform supports the development of custom Apps and extensions through its developer documentation and resources.

**Network Analysis in Biology**: Cytoscape is widely used in molecular and systems biology, genomics, and proteomics research. The software supports the analysis of molecular and genetic interaction data, functional annotations, and curated pathway datasets. Users can visualize and analyze biological networks to gain insights into complex biological processes.

**Social Network Analysis**: Cytoscape is also used for social network analysis in the field of social sciences. The software provides tools for analyzing and visualizing social networks, including options for community detection and centrality measures. Users can apply network analysis techniques to study social relationships and patterns.

**Semantic Web Analysis**: Cytoscape supports the analysis of semantic web data and ontologies. Users can import and visualize RDF and OWL data and perform semantic network analysis. The software provides tools for exploring relationships and hierarchies within semantic networks.

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.

Databox is an analytics platform for businesses, used to centralize data in one place and then visualize, track, analyze, and report on key metrics across an organization.

Starter

Professional

Growth

Premium

Spotfire, formerly known as TIBCO Spotfire, is a visual data science platform that combines visual analytics, data science, and data wrangling, so users can analyze data at-rest and at-scale to solve complex industry-specific problems.

Spotfire Cloud - Analyst

Spotfire Cloud - Business Author

Spotfire for Amazon Web Services

Spotfire Platform

Spotfire Cloud Enterprise

Spotfire Cloud - Consumer

Spotfire

Cytoscape

Get your free copy of the 2019 Buyer's Guide to Business Intelligence for tips, advice, and product info.

Need help deciding which BI tool is best for you?

Network Biology: Introduction to STRING and Cytoscape

Cytoscape: cyto-Hubba Demo Video (watch in HD is recommended)

Cytoscape.js Navigation Panel demo

Cytoscape 3.8.0 demo feat. virus-host network, stringApp, text mining, and Pharos drug target data

Official plugin here: https://github.com/cytoscape/cytoscape.js-navigator

Old links:
Source https://github.com/bumbu/cytoscape.js/tree/navigator/src/plugins
Documentation with demo https://github.com/bumbu/cytoscape.js/blob/navigator/src/plugins/jquery.cytoscape-navigator.md
Debug demo http://bumbu.github.io/cytoscape.js/debug/

Cytoscape Navigator Preview

CytoITMprobe Demo

Demo Cytoscape

MiMI-Cytoscape in Chinese part 2

Cytoscape Bird's eye Demo

cytoscape loadiq demo

Cytoscape Demo

Variation app for Cytoscape 3 early demo

Open Source

Overview of the Cytoscape Ecosystem

This video provides an overview of the status of the Cytoscape Ecosystem as of January 2022

Data Discovery and Visualization is the analysis of multiple data sources in a search for patterns and outliers and the ability to represent the data visually.

Pre-built visualization formats (heatmaps, scatter plots etc.)

Pre-built visualization formats are canned visualization types that can be selected to visualize different kinds of data.

Location Analytics / Geographic Visualization

Location analytics is the visualization of geographical or spatial data.

Predictive Analytics

Predictive Analytics is the ability to build forecasting models based on existing data sets.

Support for Machine Learning models

Machine learning refers to computer programs that can learn when exposed to new data.

Pattern Recognition and Data Mining

Pattern recognition and data mining mean the ability to recognize hidden patterns in large quantities of data.

Integration with R or other statistical packages

BI Standard Reporting

Standard reporting means pre-built or canned reports available to users without having to create them.

Customizable dashboards

Customizable dashboards are dashboards providing the builder some degree of control over the look and feel and display options.

Report Formatting Templates

Pixel Perfect reports

Pixel Perfect reports are highly-formatted reports with graphics and ability to preview the report before printing.

Ad-hoc Reporting

Ad-Hoc Reports are reports built by the user to meet highly specific requirements.

Drill-down analysis

Drill down analysis is the ability to get to a further level of detail by going deeper into the hierarchy.

Formatting capabilities

Ability to format output e.g. conditional formatting, lines, headers, footers.

Predictive modeling

Predictive modeling is the ability to build future forecasting models.

Integration with the open-source R predictive modeling environment.

Report sharing and collaboration

Report sharing and collaboration is the ability to easily share reports with others.

Report Output and Scheduling

Ability to schedule and manager report output.

Publish to Web

Publish to PDF

Output Raw Supporting Data

Report Versioning

Report versioning is the assignment of version numbers to each version of a report to help in tracking.

Report Delivery Scheduling

Report Delivery Schedule is the ability to have reports delivered to a destination at a specific data and time.

Delivery to Remote Servers

Ability to deliver reports to remote servers

TrustRadius is a technology and business research firm based in Austin, Texas. The company is known as a review platform for verified B2B technology and software reviews through a proprietary algorithm and human verification.

TrustRadius

Home

Data Discovery and Visualization Platforms

Cytoscape
Formerly cytoscape

Overview

What is Cytoscape?