Welcome to SAMMIpy¶
SAMMIpy is a tool for visualizing metabolic networks and metabolic network simulations using SAMMI directly from Python using the COBRApy toolbox. This documentation describes the Pythons wrapper for this visualization. You can view the full documentation for SAMMI here, and the documentation for COBRApy 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¶
SAMMIpy can be installed via
pip by running the following code in the command window:
pip install sammi
To update the package use:
pip install sammi -U
To use the package add the following code to your python script:
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.
- 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. Type-III Pathways
- 11. Metabolic Adaptation