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 |
| URL | https://bioinformatics.mdanderson.org/Software/SAMMI/ |
| Documentation | https://sammi.readthedocs.io/en/latest/ |
| 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. |
| 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 using the SAMMI interface, or by uploading metabolic reconstructions. Metabolic reconstructions are available through a number of databases, including BiGG , MetExplore , Human Metabolic Atlas , and Virtual Metabolic Human , 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 .
COBRA Compatibility
The COBRA toolbox has become one of the main toolboxes for the analysis of constraint-based metabolic networks, and has been developed for MATLAB , Python , and Julia . 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
Python plugin: https://sammipy.readthedocs.io/en/latest/index.html