Package: mminte
MMinte(pronounced /‘minti/) is a set of widgets that allows you to explore
the pairwise interactions (positive or negative) that occur in a microbial
community. From an association network and 16S rDNA sequence data,MMinteidentifies corresponding genomes, reconstructs metabolic models, estimates
growth under specific metabolic conditions, analyzes pairwise interactions,
assigns interaction types to network links, and generates the corresponding
network of interactions.InstallationUse pip to installMMintefromPyPI(we recommend doing this inside avirtual environment):pip install mminteNote thatMMinterequires cobrapy 0.5.11. Python versions 2.7.11+, Python 3.5+,
or Python 3.6+ are recommended.Virtual environment installationHere are step-by-step instructions for installingMMintein a virtual environment.If virtualenvwrapper is not installed,follow the directionsto install virtualenvwrapper. You should alsoupdate your shell startup file.Note on macOS El Capitan there is a known problem with the virtualenvwrapper
dependency on the six package. For a work-around use this command:$ pip install virtualenvwrapper –upgrade –ignore-installed sixCreate a virtualenv forMMintewith these commands:$ mkvirtualenv mminteUse the--pythonoption to select a specific version of Python for the
virtualenv. For example,python=python3to select the current python3
installed on the system.Note on macOS, matplotlib requires Python be installed as a framework but
virtualenv creates a non-framework build of Python. See thematplotlib FAQfor details on a workaround.Upgrade pip and setuptools to the latest versions with this command:(mminte)$ pip install --upgrade pip setuptoolsInstall the baseMMintepackage with this command:(mminte)$ pip install mminteIf you want to verify the installation with the included tests, install the
test dependencies and run the tests with these commands:(mminte)$ pip install mminte[test]
(mminte)$ pytest mminte -vWhen you are done usingMMinte, you can switch back to the system-installed
version of Python with this command:(mminte)$ deactivateStart theMMintevirtualenv again with this command:(mminte)$ workon mminteHow to run an analysis with MMinteThere are two ways to run an analysis withMMinte.In a notebookA tutorial of how to useMMinteis provided in a Jupyter notebook. Here’s how to
start Jupyter and run the notebook from the virtual environment.Install Jupyter with this command:(mminte)$ pip install jupyterInstall a kernel that uses the virtualenv installation with this command:(mminte)$ ipython kernel install --name "MMinte" --userStart the Jupyter notebook server with this command:(mminte)$ jupyter notebookJupyter opens a web page in your default browser with a file browser.Navigate to the folder whereMMinteis installed (usepip show mminteto
find the folder) and in the “notebooks” folder click on the “tutorial.ipynb”
notebook.After the notebook opens, from the “Kernel” menu, select “Change kernel” and
click on “MMinte”.Now you can run the cells in the notebook.In a web browserMMinteincludes a web site that allows you to run each widget from a web browser.
The web site runs on your local system and requires that you use a folder on the
local system for storing the results of the analysis. Here’s how to start the web site:Install the additional packages needed for the web site interface with this command:(mminte)$ pip install mminte[site]Start the web server with this command:(mminte)$ launchMMinte
Logging to "/var/folders/pz/r04ddhtx6vgb48tg0dn5cys8vz00jn/T" folder
[14/Apr/2017:14:25:04] ENGINE Listening for SIGHUP.
[14/Apr/2017:14:25:04] ENGINE Listening for SIGTERM.
[14/Apr/2017:14:25:04] ENGINE Listening for SIGUSR1.
[14/Apr/2017:14:25:04] ENGINE Bus STARTING
CherryPy Checker:
The Application mounted at '' has an empty config.

[14/Apr/2017:14:25:04] ENGINE Started monitor thread 'Autoreloader'.
[14/Apr/2017:14:25:04] ENGINE Started monitor thread '_TimeoutMonitor'.
[14/Apr/2017:14:25:04] ENGINE Serving on http://127.0.0.1:8080
[14/Apr/2017:14:25:04] ENGINE Bus STARTEDWhen you see theENGINE Bus STARTEDmessage, the web server is ready.If another service is using port 8080, you can start the web server on a different
port with this command:(mminte)$ launchMMinte --port 8099Open a web browser and go tohttp://localhost:8080(change the port number
if you started the web server on a different port) and follow the directions to
run your analysis.Release NotesVersion 1.0.3 (June 27, 2017)Added save_model_to_file() functionAdded apply_medium() function to default importVersion 1.0.2 (May 18, 2017)Updated handling of objectives for compatibility with cobra 0.6Fixed display of interaction network visualization when using different analysis
folder in web site interfaceVersion 1.0.1 (May 5, 2017)Updated directions for virtual environment installationUpdated version dependency for mackinacFixed reading files with different newline charactersAdded notebooks to package distribution and updated directionsVersion 1.0 (April 17, 2017)Refactor oforiginal MMintewitha simpler interface for functions,multiprocessing support for creating interaction models and calculating growth rates,updated web site that uses new version of DataSpyre,documentation in Jupyter notebooks,a test suite,reorganized repository to enable installation with pip.How to cite MMinteIf you useMMintefor an analysis, please cite this paper:MMinte: an application for predicting metabolic interactions among the microbial
species in a communityAdditional ReferencesThe models provided in the mminte/test/data folder are fromAnoxic Conditions Promote
Species-Specific Mutualism between Gut Microbes In Silico.The 16S sequences included in the database were provided by Maulik Shukla on
the 3rd of November of 2015.