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List of systems biology visualization software

Topic: Biology

 From HandWiki - Reading time: 2 min

Online software

Name Description Site
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
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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