List of systems biology visualization software

Online software

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

Applications

Name DescriptionOSLicenseSite
BioTapestry interactive tool for building, visualizing, and simulating genetic regulatory networks multiplatform (Java-based)LGPL
Cytoscape data integration, network visualization, and analysis multiplatform (Java-based)LGPL
GenMAPP visualize and analyze genomic data in the context of pathways WindowsApache License
MATLAB tool for modeling, simulating, and analyzing dynamic biological systems Windows, Linux, macOS Proprietary
MEGA free, online, open-source, phylogenetic analysis, drawing dendrograms etc. Windows/DOS-Win/Mac/LinuxShareware
PathVisio tool for displaying and editing biological pathways multiplatform (Java-based)Apache License
InCroMAP tool for the integration of omics data and joint visualization of experimental data in pathways multiplatform (Java-based)LGPL
Pathview pathway based data integration and visualization, easy to use and integrate into pathway analysis multiplatform (R/Bioconductor)GPL
Systrip analysis of time-series data in the context of biological networks Windows, LinuxLGPL, GPL

References

  1. Koblitz J, Schomburg D and Neumann-Schaal M.,"MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context ", F1000Research, July 17, 2020.
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