Roadmap

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This document is here for legacy information. Planning for code changes is now managed by the GitHub Issue Tracker.

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cyREST Roadmap

History

• 7/11/2016 - Future version planning start

Status

• cyREST version: 3.3.4
• REST API version: v1

Current API Status

• API implementation status as Google Doc

Status

As of July 2016, cyREST has access to Cytoscape core features including:

• API to access basic Cytoscape data objects:
  • CyNetworks
    • Nodes
    • Edges
  • CyTables
  • Visual Styles
  • Groups
• API to execute basic Cytoscape tasks:
  • Apply Visual Style
  • Apply layouts
  • Apply edge bundling
  • Get network as PNG/PDF/SVG image

Future Plan

URGENT: Fix URL loading bug

Current version cannot load any remote data sources without correct extension. This requires update to the core.

CX Support

We need to make CX as the primary data format for network data exchange. Cytoscape.js format will be supported in the future versions, but mainly for data visualization.

Collection (Root Network) API

• Experimental version is available
• Review and merge to the next release

Support for more data formats

• CSV/TSV (POST/PUT tables and networks)

API V2 (TBD)

• Command API
  • JSON output for all commands instead of human-readable HTML!
  • Requires review of new JSON structure for passing parameters to command

Documentation

• Use Swagger for API documentation
• Consolidate examples and API documents
  • Currently, API documentation is limited. Some of the parameters, especially for POST and PUT, are still not clear for first time users.
  • In short, we need something like this
  • Summer student's project?

Snippets and Examples

• This is the summer student's project
• Write more biology-oriented workflows using 3rd party tools
• Cookbook - Maybe integrated with Swagger API document
• Target Languages
  • Python
  • R
  • JavaScript
    • This is necessary if we support menu injection from web applications

Publication

• Done!