Installing pyNBS

What Python dependencies do I need to install to run pyNBS?

Currently, pyNBS requires any version of Python 2.7 and the following dependencies:

• Lifelines 0.9.1+
• NetworkX v2.0+
• Numpy 1.11.0+
• Matplotlib 1.5.1+
• MKL 1.1.2+*
• Pandas 0.19.0+
• Scipy 0.17.0+
• Scikit-learn 0.17.1+
• Seaborn 0.7.1+

*Note regarding the "MKL" package: If the user does not already have this package, we highly recommend using the Anaconda distribution of Python 2.7 (described below) to install MKL. MKL is not necessarily required for pyNBS to run (only applicable for computers with Intel processors), but if running the command line script for pyNBS, it will be necessary if the user would like to limit the number of threads used by the pyNBS process.

How do I install Python and the dependencies needed to run pyNBS?

If you do not already have Python 2.7 installed, we recommend that you download and install the Anaconda Distribution of Python 2.7. Installing this Python distribution will also install 7 of the 8 dependencies of this package mentioned above. Instructions for installing the latest Anaconda Python 2.7 distribution can be found here. The only missing dependency from this Python distribution is the Lifelines package, and instructions for Lifelines can be found on their documentation page here.

If you already have Python 2.7 installed, but are missing some of the dependencies described above, we recommend that you visit the the documentation pages linked above and follow their instructions to install the individual packages you are missing. If you have challenges installing the packages above, we recommend re-installing Python 2.7 using the Anaconda distribution.

Will pyNBS run in Python 3?

Unfortunately, we do not believe that pyNBS will work with Python 3 at this time. As the dependencies of pyNBS begin to no longer support Python 2.7 or deprecate old functions, we will attempt to migrate the code base to support Python 3.

How do I install the pyNBS package?

In order to install the pyNBS package from this repository, please follow these steps:

1. Install Python 2.7 and the required dependencies described above.
2. Clone the repository to your local drive.
3. Navigate into the root folder of the pyNBS directory on your local drive
4. Execute following command:
   python setup.py install

How do I use the pyNBS package?

There are two ways to perform the NBS algorithm with the pyNBS package:

• From a Jupyter notebook
• From a command line script