Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Visualization and reporting

Cytoscape

Desktop network visualization and analysis for exploring MS molecular networks alongside feature annotations and sample metadata.

Platform-independentDesktop graphical interfaceOpen source
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Overview

Cytoscape displays supplied nodes, edges and associated tables. In MS metabolomics it supports inspection and presentation of molecular networks generated upstream, with styles that encode sample groups or annotations. The desktop platform and its separately installed apps have distinct capabilities; a network viewer does not itself establish spectral matches.

What can this tool do?

Network visualizationInteractive dashboard

Common uses

  • Style GNPS networks using study metadata.
  • Inspect connected components and export publication figures.

Scientific fit

Primary function

Visualization and reporting

Data compatibility

Inputs

Feature or peak table, Pathway or reaction data

Outputs

Human-readable report

Input formats

Network edge lists, GraphML and node/edge attribute tables

Output formats

Cytoscape session (.cys), network/table exports and figures

Scope and considerations

Designed for

  • Exploration of supplied graphs and linked attribute tables.

Not designed for

  • Raw MS peak picking or confirmation of metabolite identity.

Important requirements

  • An upstream network, stable node identifiers and matching metadata.
  • A compatible desktop installation and any required apps.

Considerations

  • Check node identifiers when joining quantitative tables.
  • Edge definitions and filtering come from upstream analysis; layout distances are not chemical evidence.

Education

Learn this tool

External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.

NTMSS2026 Day4 S3 - Daniel Petras - ChemProp and Data Integration in CytoscapeFunctional Metabolomics Lab · Video Workshop · Needs reviewNTMSS2026 Day3 S1 - Anelize Bauermeister - Network Vizualization in CytoscapeFunctional Metabolomics Lab · Video Workshop · Needs review

Browse all education resources →

Access and documentation

Primary accessDocumentationDownload

Open-source desktop application. Use the installer and Java requirements for the selected release; apps can have separate licenses and compatibility requirements.

License: LGPL-2.1

From tool to strategy

Strategies using Cytoscape

Feature-Based Molecular Networking (FBMN)Molecular-family discovery · Nature MethodsIon Identity Molecular Networking (IIMN)Metabolite annotation · Nature Communications

Evidence and review

Official project documentation and direct tool publications reviewed on 2026-09-12. Included for downstream MS metabolomics. No installation, dataset analysis or independent performance benchmarking performed.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Shannon P, et al. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 13, 2498-2504 (2003). doi:10.1101/gr.1239303

Related tools

GNPSIntegrates with · GNPS molecular networks are commonly exported to Cytoscape.GNPS2 Cytoscape BridgeIntegrates with · GNPS2 bridge can create ready-to-open Cytoscape sessions.GraphiaAlternative to · Graph exploration and correlation-network analysis for processed MS metabolomics tables and existing networks.MetGemComplementary to · Local desktop generation and exploration of MS/MS similarity networks and two-dimensional spectral projections.MolNetInvertComplementary to · Create metadata-based molecular networks from GNPS networks or feature tables to explore how metabolites are distributed across sample groups.CorrOmicsIntegrates with · Explore associations between paired metabolomics and other omics feature tables and export correlation networks.MetScapeIntegrates with · Cytoscape app for interpreting identified metabolites and expression data in metabolic and correlation networks.

Entry history

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

  1. 2026-09-12 · First committed entry

    Add network visualization specialists and curated relationships

    View change · Entry at this revision

Full GitHub history