JATNIpy

Justin’s, Andrea’s, and Torbjörn’s network inference package for Python Nordlinglab JATNIpy

Why JATNIpy?

We re-implemented GeneSPIDER toolbox and chose Python as our programming language. Python is a popular high-level programming language. It is freely available and widely used by academic and commercial.

Results:

We incorporate several free available python packages and refer the package called scikit-grni into a new complete package. We finally name the new complete package as JATNIpy.

Availability and Implementation: Source code freely available for download at https://bitbucket.org/temn/JATNIpy/, reimplemented GeneSPIDER toolbox in Python.

How do I get set up?

• Alternative 1: Use git to fetch JATNIpy repository run this command

git clone https://bitbucket.org/temn/JATNIpy/

• Alternative 2: Download it from JATNIpy
• Alternative 3: Use the pip3 to install JATNIpy from Pypi

	pip3 install jatnipy -t ~/JATNIpy

~/JATNIpy is the folder that you want to download. Then, change to the directory where you downloaded from the repository by

	cd ~/JATNIpy/jatnipy.

Before we uses JATNIpy, we should make sure pip3 has been installed in local computer. If there is not pip in local computer, we use the following command to install it.

• *For Debian/Ubuntu user:

	apt-get install python3-pip

• *For CentOS 7 user:

	yum install python34-setuptools
	easy_install pip

After we make sure pip3 is in our local computer, we then install virtualenvwrapper to create a virtual environment for our local computer by these commands

	pip3 install virtualenvwrapper
	export WORKON_HOME=~/Envs
	mkdir -p $WORKON_HOME
	source /usr/local/bin/virtualenvwrapper.sh
	mkvirtualenv env1
	workon env2

Create the new virtual environment env1 by mkvirtualenv env1 Choose the virtual environment you want to work on by workon env1 After working on the environment you want, then use pip3 to install the open source python3 packages with the command

	pip3 install -e

• Dependencies:

  • git Version control system for tracking the development of programming
  • Scipy Python-based software for mathematics, science, and engineering
  • Numpy Fundamental python package for doing numerical or mathematics computation
  • pandas Using data structures and data analysis tools easily in Python
  • matplotlib Useful Python 2D plotting tool which provides MATLAB-like interface
  • scikit-learn Data mining and data analysis which built on Numpy, Scipy and matplotlib
  • networkx Python package which is made for studying graphs and the complex networks
  • glmnet_py The popular glmnet library for Python version
  • py-ubjson Universal Binary JSON encoder/decoder for Python version
  • CVXPY Handling convex optimization problems for Python version
  • Requests: HTTP for Humans Python library for requesting HTTP

• Datasets are available here.

• Networks are available here.

Contact: Justin, Andreas Tjärnberg, Torbjörn Nordling