Preparing your computer for the course

Owned by Erick Peirson (Unlicensed)
Last updated: Apr 29, 2016

This how-to will walk you through setting up your computer for this course. If you are using a computer with Mac OSX or Linux (e.g. Ubuntu), you can proceed with the tutorial below. If you're stuck with windows, please see Help! I'm stuck with Windows :-(.

If you run into trouble, see Getting Help.

Everybody

  1. Install Anaconda Python 2.7. Anaconda is a distribution of Python, a popular programming language for scientific computing. Anaconda comes pre-loaded with over 300 awesome Python packages (libraries), so it really cuts down on set-up time. Be sure to select Python 2.7, NOT Python 3.4.
  2. Install Atom. Atom is a slick text editor. 
  3. Install Java 8.
  4. Install the latest version of Firefox web browser.
  5. Install the Zotero Firefox Plugin. Zotero is a bibliographic metadata management tool with some nifty features. We'll use it to build corpora from online databases. Be sure to install the plugin for Firefox!
  6. Install ImageMagick.  This package provides all kinds of nifty tools for working with images. We'll need it work with PDFs later on.
    • OSX: From the terminal, do:
      • brew install imagemagick
    • Ubuntu Linux: From the terminal, do:
      • sudo apt-get install imagemagick
  7. Install Xpdf. Command-line tools for working with PDFs.
  8. Install Tesseract OCR. Tesseract is an open source engine for Optical Character Recognition (OCR). We'll use this to extract plain-text from PDFs.
    • OSX: From the terminal, do:
      • brew install tesseract --all-languages
    • Ubuntu Linux: see this page.
  9. SmartGit. This is a great tool for working with Git repositories.
  10. Install Cytoscape (http://cytoscape.org/)
  11. Install NLTK Corpora. Follow the instructions at http://www.nltk.org/data.html#command-line-installation.
  12. Download Stanford NER.
  13. Tethne. Once you have installed Anaconda (or Python 2.7 + setuptools), you should be able to install Tethne from the terminal via pip: 
    1. $ pip install tethne

Mac OSX

  1. Install Homebrew. Homebrew is a package manager that makes it easy to install software from the command line.