Welcome to SAMMIM

SAMMIM is a tool for visualizing metabolic networks and metabolic network simulations using SAMMI directly from MATLAB using the COBRA toolbox. This documentation describes the MATLAB wrapper for this visualization. You can view the full documentation for SAMMI here, and the documentation for COBRA here.

If you use SAMMI for your project, please cite the following publication: Schultz, A., & Akbani, R. (2019). SAMMI: A Semi-Automated Tool for the Visualization of Metabolic Networks. Bioinformatics.

Installation and Usage

To use this tool simply add the SAMMIM folder to your MATLAB path. There is no need to add its subfolders. For a short description of how to use the plotting function type:

help sammi

Some of the functionality available in SAMMI, such as PDF download and data upload, are not directly available though this plugin. To use these functions download the model in a SAMMI format and upload the file in the SAMMI web interface at www.SammiTool.com.

For a full description of this plugin please refer to the remaining sections of this documentation.

Documentation

• Structure Arrays
  • Parser
  • Data
  • Options
• Functions
  • Plotting
  • Opening a visualization
  • Running SAMMIM examples
• Examples
  • 0. Plot entire model
  • 1-2. Divide the model into subgraphs using model annotation
  • 3. Plot and visualize multiple maps
  • 4. Plot only user-defined reactions
  • 5. Shelve secondary metabolites on load
  • 6. Plot multiple user-defined subgraphs
  • 7-8. Data mapping
  • 9. Change map upon load
  • 10. Load Existing Map
  • 11. Type-III Pathways