List of systems biology visualization software

Last updated

Contents

Online software

NameDescriptionSite
GESTALT Workbenchgraphical workbench for analysis of large-scale genomic sequence data
N-Browseinteractive graphical browser for biological networks
NetPathcurated resource of human signal transduction pathways
MEGA free, online, open-source, phylogenetic analysis, drawing dendrograms etc.
REACTOMEfree, 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

NameDescriptionOSLicenseSite
BioTapestry interactive tool for building, visualizing, and simulating genetic regulatory networksmultiplatform (Java-based)LGPL
Cytoscape data integration, network visualization, and analysismultiplatform (Java-based) LGPL
GenMAPP visualize and analyze genomic data in the context of pathwaysWindowsApache License
MATLAB tool for modeling, simulating, and analyzing dynamic biological systemsWindows, Linux, macOSProprietary
MEGA free, online, open-source, phylogenetic analysis, drawing dendrograms etc.Windows/DOS-Win/Mac/LinuxShareware
PathVisio tool for displaying and editing biological pathwaysmultiplatform (Java-based)Apache License
InCroMAP tool for the integration of omics data and joint visualization of experimental data in pathwaysmultiplatform (Java-based) LGPL
Pathview pathway based data integration and visualization, easy to use and integrate into pathway analysismultiplatform (R/Bioconductor) GPL
SBMLDiagrams [2] Python API to display and edit SBML layout/render extensionmultiplatformMIT
Systrip analysis of time-series data in the context of biological networks Windows, Linux LGPL, GPL

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 . PMC   7383707 . 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. PMC   9805581 . PMID   36370074.
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