Semi-Automated Metabolic Map Illustrator¶
Welcome to SAMMI, the Semi-Automated Metabolic Map Illustrator. SAMMI is a browser based tool developed for the visualization of metabolic networks. In SAMMI, metabolic networks are illustrated by directed bipartite graphs, where reactions and metabolites represent two distinct groups of nodes. Substrate metabolites connect into reaction nodes, which in turn connect to product metabolites.
SAMMI renders metabolic maps as interactive, constantly updated force-directed graphs, allowing for efficient automated node positioning. The tool has also been developed to allow a wide array of node editing and positioning functionalities, as well as easy graph parsing and navigation. SAMMI can be used for both context-specific visualizations, where users can upload their own reaction and/or metabolite data in order to visualize the context of their own network, or to generate visually appealing models that can be easily shared among SAMMI users.
SAMMI has been implemented as a standalone tool available at www.sammitool.com, and plugins have been developed for COBRA in MATLAB and COBRApy in Python.
Introductory video¶
The following video provides a quick introduction to some of the main functionalities of SAMMI.
Documentation¶
The following documentation describes all the tools available in SAMMI.
- Loading a Map
- SAMMI Interface
- Graph Settings
- Associated Graph Data
- Node and Edge Coloring
- Node and Edge Sizing
- Mapping Other Types of Omics Data
- Secondary Metabolites
- Graph Navigation
- Downloads
- Floating Menu
- Keyboard Shortcuts
- SAMMI Map Format
- COBRA Compatibility
- Video Tutorials
- Copyright and License
- Acknowledgments
- Contact Us
- Citation