List of systems biology visualization software

## Online software

Name  | Description | Site

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GESTALT Workbench  | graphical workbench for analysis of large-scale genomic sequence data  | [1]
N-Browse  | interactive graphical browser for biological networks  | [2]
NetPath  | curated resource of human signal transduction pathways  | [3]
MEGA | free, online, open-source, phylogenetic analysis, drawing dendrograms etc.  | [4]
REACTOME  | free, online, open-source, curated pathway database encompassing many areas of human biology  | [5]
WikiPathways | curate biological pathways  | [6]
MetaboMAPS  | visualize omics data on shared metabolic pathways [1] | [7]

## Applications

Name  | Description | OS | License | Site

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BioTapestry | interactive tool for building, visualizing, and simulating genetic regulatory networks  | multiplatform (Java-based) | LGPL | [8]
Cytoscape | data integration, network visualization, and analysis  | multiplatform (Java-based) | LGPL | [9]
GenMAPP | visualize and analyze genomic data in the context of pathways  | Windows | Apache License | [10]
MATLAB | tool for modeling, simulating, and analyzing dynamic biological systems  | Windows, Linux, macOS  | Proprietary  | [11]
MEGA | free, online, open-source, phylogenetic analysis, drawing dendrograms etc.  | Windows/DOS-Win/Mac/Linux | Shareware | [12]
PathVisio | tool for displaying and editing biological pathways  | multiplatform (Java-based) | Apache License | [13]
InCroMAP  | tool for the integration of omics data and joint visualization of experimental data in pathways  | multiplatform (Java-based) | LGPL | [14]
Pathview  | pathway based data integration and visualization, easy to use and integrate into pathway analysis  | multiplatform (R/Bioconductor) | GPL | [15] [16]
SBMLDiagrams[2] | Python API to display and edit SBML layout/render extension | multiplatform | MIT | [17]
Systrip | analysis of time-series data in the context of biological networks  | Windows, Linux | LGPL, GPL | [18]

## References

1. ↑ Koblitz, Julia; Schomburg, Dietmar; Neumann-Schaal, Meina (2020). "MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context". F1000Research 9: 288. doi:10.12688/f1000research.23427.2. PMID 32765840.
2. ↑ Xu, Jin; Jiang, Jessie; Sauro, Herbert M (1 January 2023). "SBMLDiagrams: a python package to process and visualize SBML layout and render". Bioinformatics 39 (1): btac730. doi:10.1093/bioinformatics/btac730. PMID 36370074.

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