DynamicGut simulates microbial interactions in a community over time given a specific diet.
Please use the cobrapy Google Group for help. Alternatively, you can use gitter.im for quick questions and discussions (faster response times).
More information about opencobra is available at the website.
Use pip to install DynamicGut from PyPI (we recommend doing this inside a virtual environment):
pip install dynamicgut
- If virtualenvwrapper is not installed, follow the directions to install virtualenvwrapper.
An example of how to use DynamicGut is provided in a notebook. Here's how to start Jupyter and run the notebook from the virtualenv.
The three models in the "test/data" folder come from AGORA along with the initial_unhealthy_diet.
- cobrapy doi:10.1186/1752-0509-7-74
- ModelSEED doi:10.1038/nbt.1672
- PATRIC doi:10.1093/nar/gkt1099