Software Requirements (Module 2)

In addition to the software listed in Preparing your computer for the course, please install the following software before getting started:

1. Java 8
• If you don't know what version of Java you have installed, see this page (https://java.com/en/download/help/version_manual.xml) for instructions.
• To download the latest version of Java, see this page: http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html
2. Cytoscape (http://cytoscape.org/)
3. Python 2.7
• I highly recommend installing Anaconda Python 2.7 (https://www.continuum.io/downloads). This will install Python, along with oodles of useful scientific computing packages. Note: install version 2.7, NOT version 3.5.
• If you don't want to use Anaconda, be sure that you have the following packages installed:
• Python 2.7: https://www.python.org/downloads/
• Setuptools: https://pypi.python.org/pypi/setuptools
• iPython (Jupyter) Notebook: http://jupyter.readthedocs.org/en/latest/install.html 
• Follow the instructions for Python 2.
• MatPlotLib: http://matplotlib.org/faq/installing_faq.html#how-to-install
• NLTK: http://www.nltk.org/install.html
4. NLTK Corpora: follow the instructions at http://www.nltk.org/data.html#command-line-installation to install all NLTK corpora.
5. Tethne
• Once you have installed Anaconda (or Python 2.7 + setuptools), you should be able to install Tethne from the terminal via pip: 
• $ pip install tethne