List of systems biology visualization software
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Online software
| class="wikitable"
! Name ! Description | Site |
| GESTALT Workbench
| graphical workbench for analysis of large-scale genomic sequence data | [http://db.systemsbiology.net/gestalt/] |
| N-Browse
| interactive graphical browser for biological networks | [http://aquila.bio.nyu.edu/NBrowse2/NBrowse.html] |
| NetPath
| curated resource of human signal transduction pathways | [http://www.netpath.org/] |
| MEGA
| free, online, open-source, phylogenetic analysis, drawing dendrograms etc. | [http://www.megasoftware.net/] |
| REACTOME
| free, online, open-source, curated pathway database encompassing many areas of human biology | [http://www.reactome.org/] |
| WikiPathways
| curate biological pathways | [http://www.wikipathways.org/] |
| MetaboMAPS
| visualize omics data on shared metabolic pathways {{Cite journal|doi = 10.12688/f1000research.23427.2|title = MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context|year = 2020|last1 = Koblitz|first1 = Julia|last2 = Schomburg|first2 = Dietmar|last3 = Neumann-Schaal|first3 = Meina|journal = F1000Research|volume = 9|page = 288|pmid = 32765840|pmc = 7383707 | doi-access=free }} | [https://metabomaps.brenda-enzymes.org/] |
Applications
| class="wikitable"
! Name ! Description | OS | License | Site | |
| BioTapestry
| interactive tool for building, visualizing, and simulating genetic regulatory networks | multiplatform (Java-based) | LGPL | [http://www.biotapestry.org] | |
| Cytoscape
| data integration, network visualization, and analysis | multiplatform (Java-based) | LGPL | [http://www.cytoscape.org/] | |
| GenMAPP
| visualize and analyze genomic data in the context of pathways | Windows | Apache License | [http://www.genmapp.org/] | |
| MATLAB
|tool for modeling, simulating, and analyzing dynamic biological systems |Windows, Linux, macOS |Proprietary |[https://www.mathworks.com/products/simbiology.html] | ||||
| MEGA
| free, online, open-source, phylogenetic analysis, drawing dendrograms etc. | Windows/DOS-Win/Mac/Linux | Shareware | [http://www.megasoftware.net/] | |
| PathVisio
| tool for displaying and editing biological pathways | multiplatform (Java-based) | Apache License | [http://www.pathvisio.org/] | |
| InCroMAP
| tool for the integration of omics data and joint visualization of experimental data in pathways | multiplatform (Java-based) | LGPL | [http://www.cogsys.cs.uni-tuebingen.de/software/InCroMAP/] | |
| Pathview
| pathway based data integration and visualization, easy to use and integrate into pathway analysis | multiplatform (R/Bioconductor) | GPL | [http://pathview.r-forge.r-project.org/] [http://bioconductor.org/packages/release/bioc/html/pathview.html] | |
| SBMLDiagrams{{cite journal |last1=Xu |first1=Jin |last2=Jiang |first2=Jessie |last3=Sauro |first3=Herbert M |title=SBMLDiagrams: a python package to process and visualize SBML layout and render |journal=Bioinformatics |date=1 January 2023 |volume=39 |issue=1 |pages=btac730 |doi=10.1093/bioinformatics/btac730|pmid=36370074 |pmc=9805581 }} | Python API to display and edit SBML layout/render extension | multiplatform | MIT | [https://github.com/sys-bio/SBMLDiagrams] |
| Systrip
| analysis of time-series data in the context of biological networks | Windows, Linux | LGPL, GPL | [https://tulip.labri.fr/TulipDrupal/?q=systrip] |