1.0.2

fixed

• Fix mcp app reload during restart of desktop to be consistent, it was susceptible to be skipped due to race conditions in osgi timing and as a result mcp service was not started. pull/8

1.0.1

fixed

• Fixed app init after installing app into a running instance of desktop. The app init routine wasn't getting triggered to render the toolbar icon for mcp and start the etl service, had to restart desktop. This fixes the behavior to force app init to run after install on current desktop. pull/6

1.0.0

Added

• TableImportFile mcp tool, pull/5

Notes

• This is the culmination fo all prior rc releases and is first GA release. T
• The current mcp tools are capable of completing the RNA Sequence Analysis Tutuoral as a benchmark of level of integration.

Try it!

Refer to README.md for installation, agent configuration and usage instructions.

1.0.0-rc.4

Added

• Add 3 new tools for using desktop commands from llm: CommandGatewayGetTool, CommandGatewayInvokeTool, CommandGatewaySearchTool, pull/3

Notes

• When installing this app jar into cytoscape, make sure to remove any older cytoscape-mcp-1.0.0* jars first.
• MCP Tool Manifest
• there is a known issue with table import file command invocation getting errors regardless of input parameter combinations.

1.0.0-rc.3

Added

• Claude Desktop extension bundle (cytoscape-mcp.mcpb) added to enable stdio bridge configuration to Cytoscape's MCP HTTP server, use make build_claude_mcpb
• 10 new MCP tools added for visual style mapping and data column interrogation: get_mappable_properties, get_compatible_columns, get_styles, switch_current_style, get_column_range, get_column_distinct_values, create_continuous_mapping, create_discrete_mapping, create_discrete_mapping_generated, create_passthrough_mapping
• refer to MCPManifest.md for detailed descriptions of each MCP tool.

Fixed / Changed

• load_cytoscape_network_view refactored from optional parameters to a ConditionalParameter model for improved LLM input guidance and more reliable parameter resolution
• Fixed conditional parameter processing on load_cytoscape_network_view to correctly handle waived vs. provided states
• Added inferred data types on tabular file column inspection and enforced a maximum-size cap on column value retrievals
• Revised tool descriptions across the manifest to remove direct tool-name self-references for cleaner LLM context
• Discrete mapping generator color input made conditional; node size is now locked when a size-based style mapping is applied
• Fixed stdio bridge timeout in the Claude Desktop extension
• Updated to mcp sdk 1.1.0, updated McpTransportProvider to follow the latest from 1.1.0.

Try it!

Refer to README.md for installation, agent configuration and usage instructions.

Note - Claude Dekstop Usage

Specific for just Claude Desktop installation an extension bundle file is provided - cytoscape-mcp.mcpb as a downloadable artifact on this release. This bundle handles connection to Cytoscape MCP. Installation instructions for cytoscape-mcp.mcpb are provided here - Claude Desktop Config

Agent prompt examples to activate Cytoscape MCP tools

• discrete mapping
  • > map edge shape to interaction
  • > map weight to node size
  • > generate green colors on edges based on discrete values of confidence
• continous mapping
  • > set color gradient on nodes from blue to red based on eccentricity
• pass through mapping
  • > set node label to gene1
• manage styles
  • > switch network style
  • > switch network style to default

1.0.0-rc.2

Added

• Initial release candidate of the Cytoscape MCP Server app
• Embedded MCP (Model Context Protocol) server hosted inside Cytoscape Desktop CyRest HTTP server. MCP supprots Streamable HTTP transport.
• 9 MCP tools initially added related to loading and analyzing a network on desktop: get_loaded_network_views, set_current_network_view, create_network_view, load_cytoscape_network_view, inspect_tabular_file, get_file_columns, analyze_network, get_layout_algorithms, apply_layout
• 2 MCP tools added for reading and updating properties of network default style: set_visual_default, get_visual_style_defaults
• refer to MCPManifest.md for detailed descriptions of each MCP tool.

Try it!

• refer to README.md for installation, agent configuration and usage instructions.
• Sample agent prompts to activate the tools:
  • > open a network using cytoscape desktop
  • > analyze the network
  • > change the network layout
  • > increse the network edge width by 1
  • > change the network node color to green
  • > change node label to courier new
  • > what properties can I lock on network
  • > lock node width and height on network

1.0.0-rc.1

Added

• Initial release of the Cytoscape MCP Server app
• Embedded MCP (Model Context Protocol) server running inside Cytoscape Desktop CyRest HTTP (Streamable HTTP transport) — no separate server process required
• 9 MCP tools initially added related to loading and analyzing a network on desktop: get_loaded_network_views, set_current_network_view, create_network_view, load_cytoscape_network_view, inspect_tabular_file, get_file_columns, analyze_network, get_layout_algorithms, apply_layout
• refer to MCPManifest.md for detailed descriptions of each MCP tool.

Try it!

• refer to README.md for installation and usage instructions.
  The agent prompt can be simply:

   > analyze new network in cytoscape desktop