Cytoscape Web Development Priorities - cytoscape/cytoscape-web GitHub Wiki

This document outlines the prioritized list of features and enhancements planned for implementation in Cytoscape Web within the next year. Features are listed in order of priority.

High Priority

  • Undo/Redo: Allows users to easily reverse or reapply recent actions in Cytoscape

  • Network analysis tools: Supporting tools such as network analyzer, clustering.

  • Support customized column and decimal separator in network importer: Allow users to set column and decimal separator in the advanced setting.

  • Import of SIF format: Implement support for importing SIF (Simple Interaction Format) files in Cytoscape Web.

  • Tutorials: Comprehensive tutorials to teach researchers how to effectively use Cytoscape Web for various research applications, following the same successful approach used for their desktop version tutorials.

  • Rendering of pie-chart on nodes: display multiple data values as proportional segments within nodes as pie a chart. Rendering only.

  • Performance improvement when rendering large networks, increase the network size Cytoscape Web can support to 100,000 elements.

  • Table View Persistence: Saves user-defined column arrangements and sorting preferences in the table browser directly to the back-end server or CX2 file, ensuring your customized data organization remains intact between sessions.

  • External Interaction Database Access: Direct integration with additional interaction databases beyond NDEx, providing similar database connectivity features as available in Cytoscape Desktop.

Medium Priority

  • Publish App API v1.0: Stabilize and publicly release the Cytoscape Web API documentation to enable broader community development and integration, transitioning from the preliminary version currently shared with early adopters to a robust, well-documented public release.

  • Automatic sync to cloud storage (NDEx): Updates user's networks to NDEx at regular intervals, maintaining current versions of network online while allowing users to disable this functionality through settings if preferred.

  • Editing of pie chart and ring chart: Editing of pie chart and ring chart in visual style editor.

  • Setting images as nodes or network background.

  • Filtering function: Enables users to selectively display network elements based on specified criteria, allowing for focused analysis of relevant nodes and edges within complex biological networks.

  • App Store integration with the desktop: The integrated App Store will provide a unified marketplace for both Cytoscape Web and Desktop users to discover, install, and manage extensions that enhance network visualization and analysis capabilities across platforms.

  • Cytoscape Web Embed: Enables integration of the Cytoscape Web functionality as an embeddable widget within external websites, allowing partners to incorporate interactive network visualization and analysis capabilities directly into their own platforms.

Low Priority

  • Reusable style: Allow users to extract and save a style and reuse it in other networks.

  • Independent Tab Workspaces: Open different Cytoscape workspaces in separate browser tabs, overcoming the current limitation where all tabs display the same workspace.