SAMMI
| Overview | |
|---|---|
| Description | SAMMI is a web-based tool for the visualization of metabolic networks and related data. Networks can be uploaded directly from KEGG annotated pathways or using constraint-based metabolic reconstructions. |
| Development Information | |
| GitHub | MD-Anderson-Bioinformatics/SAMMI (opens in new tab) |
| URL | https://bioinformatics.mdanderson.org/Software/SAMMI/ (opens in new tab) |
| Documentation | https://sammi.readthedocs.io/en/latest/ (opens in new tab) |
| Language | R |
| Current version | 0.0.1 |
| Platforms | Chrome, Firefox and Edge |
| License | GPL (>=3) |
| Status | Active |
| Last updated | 01/25/2018 |
| References | |
| Citation | Schultz A, Akbani R. SAMMI: a semi-automated tool for the visualization of metabolic networks. Bioinformatics. 2020, 36(8):2616-2617. (opens in new tab) |
| Help and Support | |
| Contact |
Andre Schultz
|
Semi-Automated Metabolic Map Illustrator
SAMMI is a tool for drawing metabolic networks and visualizing data related to such networks. Networks can be imported directly from KEGG (opens in new tab) using the SAMMI interface, or by uploading metabolic reconstructions. Metabolic reconstructions are available through a number of databases, including BiGG (opens in new tab), MetExplore (opens in new tab), Human Metabolic Atlas (opens in new tab), and Virtual Metabolic Human (opens in new tab), and through a number of publications in the literature.
Metabolic networks can be uploaded as a single network, or be parsed into subgraphs upon loading. SAMMI maps are interactive, constantly updated force-directed graphs, allowing for efficient automated node positioning. SAMMI also offers a wide array of node editing functionalities, such as node fixing, duplication of nodes, edge curving, shelving, arranging into a number of different shapes, text and shape annotations, and node coloring and sizing according to data. For a full description of all SAMMI functionalities you can read the SAMMI documentation here (opens in new tab).
COBRA Compatibility
The COBRA toolbox (opens in new tab) has become one of the main toolboxes for the analysis of constraint-based metabolic networks, and has been developed for MATLAB (opens in new tab), Python (opens in new tab), and Julia (opens in new tab). For ease of user we have developed plugins to allow users to use SAMMI directly from MATLAB and Python. To see how to install and use these plugins please refer to their respective documentations:
MATLAB plugin: https://sammim.readthedocs.io/en/latest/index.html (opens in new tab)
Python plugin: https://sammipy.readthedocs.io/en/latest/index.html (opens in new tab)