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Visualization and reporting

GNPS2 Cytoscape Bridge

Convert a GNPS2 GraphML network into a styled desktop Cytoscape session in the browser.

LC-MSWeb applicationFree web service
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Overview

The bridge packages an existing GNPS2 network with node and edge tables and sample-group styling for desktop inspection. It does not calculate spectral similarity or build the original network.

What can this tool do?

Network visualization

Common uses

  • Move an existing GNPS2 network into desktop Cytoscape.

Scientific fit

Primary function

Visualization and reporting

Data compatibility

Inputs

Human-readable report

Outputs

Human-readable report

Input formats

GNPS2 network.graphml or supported task ID/status URL

Output formats

Cytoscape .cys session

Scope and considerations

Designed for

  • GNPS2 network conversion with group styling and optional singletons.

Not designed for

  • Raw-data processing, network inference or validation of molecular identities.

Important requirements

  • Compatible GraphML or an accessible supported GNPS2 task.
  • Desktop Cytoscape to open the resulting session.

Considerations

  • Styling summarizes supplied groups; visual similarity is not chemical identification evidence.
  • Session compatibility should be checked with the installed Cytoscape version.

Access and documentation

Primary access

Public browser interface. The documented conversion runs locally in the browser; task-ID input fetches data from GNPS2. No independent execution test or software-license verification performed.

Evidence and review

Official interface documentation reviewed on 2026-09-10. No dedicated publication identified; general GNPS and Cytoscape papers are not presented as bridge publications. Cytoscape integration linked on 2026-09-12.

No dedicated scholarly publication is listed. Follow the official documentation and resource-specific citation guidance.

Software and documentation citations

  • GNPS2 Cytoscape .cys generator. Interface documentation. Accessed 10 September 2026. Documentation

Related tools

CytoscapeIntegrates with · Open generated .cys sessions in compatible desktop Cytoscape.GNPS2 Feature-Based Molecular Networking workflowIntegrates with · Accepts its GNPS2 network outputs.GNPSPart of · GNPS2 browser application.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-12 · Entry update

    Add network visualization specialists and curated relationships

    View change · Entry at this revision
  2. 2026-09-10 · First committed entry

    Add FBMN Stats and GNPS2 Cytoscape Bridge entries

    View change · Entry at this revision

Full GitHub history