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Online software
| Name | Description | Site |
|---|---|---|
| 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 |
Applications
| Name | Description | OS | License | Site |
|---|---|---|---|---|
| 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 | Windows | Apache 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/Linux | Shareware | |
| 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 | |
| SBMLDiagrams | Python API to display and edit SBML layout/render extension | multiplatform | MIT | |
| Systrip | analysis of time-series data in the context of biological networks | Windows, Linux | LGPL, GPL |
References
- 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.
- 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.