{ "info": { "author": "Helena Mendes-Soares, Michael Mundy, Luis Mendes Soares, Nicholas Chia", "author_email": "microbialmetabolicinteractions@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Microbial Metabolic Interactions\n================================\n\n**MMinte** (pronounced /\u2018minti/) is a set of widgets that allows you to explore\nthe pairwise interactions (positive or negative) that occur in a microbial\ncommunity. From an association network and 16S rDNA sequence data, **MMinte**\nidentifies corresponding genomes, reconstructs metabolic models, estimates\ngrowth under specific metabolic conditions, analyzes pairwise interactions,\nassigns interaction types to network links, and generates the corresponding\nnetwork of interactions.\n\nInstallation\n------------\n\nUse pip to install **MMinte** from `PyPI `_\n(we recommend doing this inside a `virtual environment\n`_)::\n\n pip install mminte\n\nNote that **MMinte** requires cobrapy 0.5.11. Python versions 2.7.11+, Python 3.5+,\nor Python 3.6+ are recommended.\n\nVirtual environment installation\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nHere are step-by-step instructions for installing **MMinte** in a virtual environment.\n\n1. If virtualenvwrapper is not installed, `follow the directions `_\n to install virtualenvwrapper. You should also `update your shell startup file\n `_.\n\n Note on macOS El Capitan there is a known problem with the virtualenvwrapper\n dependency on the six package. For a work-around use this command:\n\n $ pip install virtualenvwrapper --upgrade --ignore-installed six\n\n2. Create a virtualenv for **MMinte** with these commands::\n\n $ mkvirtualenv mminte\n\n Use the ``--python`` option to select a specific version of Python for the\n virtualenv. For example, ``python=python3`` to select the current python3\n installed on the system.\n\n Note on macOS, matplotlib requires Python be installed as a framework but\n virtualenv creates a non-framework build of Python. See the\n `matplotlib FAQ `_\n for details on a workaround.\n\n3. Upgrade pip and setuptools to the latest versions with this command::\n\n (mminte)$ pip install --upgrade pip setuptools\n\n4. Install the base **MMinte** package with this command::\n\n (mminte)$ pip install mminte\n\n5. If you want to verify the installation with the included tests, install the\n test dependencies and run the tests with these commands::\n\n (mminte)$ pip install mminte[test]\n (mminte)$ pytest mminte -v\n\n6. When you are done using **MMinte**, you can switch back to the system-installed\n version of Python with this command::\n\n (mminte)$ deactivate\n\n Start the **MMinte** virtualenv again with this command::\n\n (mminte)$ workon mminte\n\nHow to run an analysis with MMinte\n----------------------------------\n\nThere are two ways to run an analysis with **MMinte**.\n\nIn a notebook\n^^^^^^^^^^^^^\n\nA tutorial of how to use **MMinte** is provided in a Jupyter notebook. Here's how to\nstart Jupyter and run the notebook from the virtual environment.\n\n1. Install Jupyter with this command::\n\n (mminte)$ pip install jupyter\n\n2. Install a kernel that uses the virtualenv installation with this command::\n\n (mminte)$ ipython kernel install --name \"MMinte\" --user\n\n3. Start the Jupyter notebook server with this command::\n\n (mminte)$ jupyter notebook\n\n Jupyter opens a web page in your default browser with a file browser.\n\n4. Navigate to the folder where **MMinte** is installed (use `pip show mminte` to\n find the folder) and in the \"notebooks\" folder click on the \"tutorial.ipynb\"\n notebook.\n\n5. After the notebook opens, from the \"Kernel\" menu, select \"Change kernel\" and\n click on \"MMinte\".\n\n6. Now you can run the cells in the notebook.\n\nIn a web browser\n^^^^^^^^^^^^^^^^\n\n**MMinte** includes a web site that allows you to run each widget from a web browser.\nThe web site runs on your local system and requires that you use a folder on the\nlocal system for storing the results of the analysis. Here's how to start the web site:\n\n1. Install the additional packages needed for the web site interface with this command::\n\n (mminte)$ pip install mminte[site]\n\n2. Start the web server with this command::\n\n (mminte)$ launchMMinte\n Logging to \"/var/folders/pz/r04ddhtx6vgb48tg0dn5cys8vz00jn/T\" folder\n [14/Apr/2017:14:25:04] ENGINE Listening for SIGHUP.\n [14/Apr/2017:14:25:04] ENGINE Listening for SIGTERM.\n [14/Apr/2017:14:25:04] ENGINE Listening for SIGUSR1.\n [14/Apr/2017:14:25:04] ENGINE Bus STARTING\n CherryPy Checker:\n The Application mounted at '' has an empty config.\n\n [14/Apr/2017:14:25:04] ENGINE Started monitor thread 'Autoreloader'.\n [14/Apr/2017:14:25:04] ENGINE Started monitor thread '_TimeoutMonitor'.\n [14/Apr/2017:14:25:04] ENGINE Serving on http://127.0.0.1:8080\n [14/Apr/2017:14:25:04] ENGINE Bus STARTED\n\n When you see the ``ENGINE Bus STARTED`` message, the web server is ready.\n\n3. If another service is using port 8080, you can start the web server on a different\n port with this command::\n\n (mminte)$ launchMMinte --port 8099\n\n4. Open a web browser and go to ``http://localhost:8080`` (change the port number\n if you started the web server on a different port) and follow the directions to\n run your analysis.\n\nRelease Notes\n-------------\n\nVersion 1.0.3 (June 27, 2017)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n* Added save_model_to_file() function\n* Added apply_medium() function to default import\n\nVersion 1.0.2 (May 18, 2017)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n* Updated handling of objectives for compatibility with cobra 0.6\n* Fixed display of interaction network visualization when using different analysis\n folder in web site interface\n\nVersion 1.0.1 (May 5, 2017)\n^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n* Updated directions for virtual environment installation\n* Updated version dependency for mackinac\n* Fixed reading files with different newline characters\n* Added notebooks to package distribution and updated directions\n\nVersion 1.0 (April 17, 2017)\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nRefactor of `original MMinte `_ with\n\n* a simpler interface for functions,\n* multiprocessing support for creating interaction models and calculating growth rates,\n* updated web site that uses new version of DataSpyre,\n* documentation in Jupyter notebooks,\n* a test suite,\n* reorganized repository to enable installation with pip.\n\nHow to cite MMinte\n------------------\n\nIf you use **MMinte** for an analysis, please cite this paper:\n`MMinte: an application for predicting metabolic interactions among the microbial\nspecies in a community `_\n\nAdditional References\n---------------------\n\n1. The models provided in the mminte/test/data folder are from `Anoxic Conditions Promote\n Species-Specific Mutualism between Gut Microbes In Silico `_.\n\n2. The 16S sequences included in the database were provided by Maulik Shukla on\n the 3rd of November of 2015.", "description_content_type": null, "docs_url": null, "download_url": "https://pypi.python.org/pypi/mminte", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/mendessoares/mminte", "keywords": "metabolism biology optimization flux balance analysis fba", "license": "BSD", "maintainer": null, "maintainer_email": null, "name": "mminte", "package_url": "https://pypi.org/project/mminte/", "platform": "GNU/Linux,Mac OS X >= 10.7,Microsoft Windows >= 7", "project_url": "https://pypi.org/project/mminte/", "project_urls": { "Download": "https://pypi.python.org/pypi/mminte", "Homepage": "https://github.com/mendessoares/mminte" }, "release_url": "https://pypi.org/project/mminte/1.0.3/", "requires_dist": null, "requires_python": null, "summary": "Microbial Metabolic interactions", "version": "1.0.3" }, "last_serial": 2982921, "releases": { 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