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Installing NeuroNER requirements on Microsoft Windows

(tested on Windows 7 SP1 64-bit)

Table of Contents

Python 3.5, TensorFlow, and several other Python packages

First, install Python 3.5 64-bit and TensorFlow following these instructions: How to install TensorFlow on Windows?

Then, from the command prompt (make sure pip is connected to Python 3.5. You can verify it by running pip -V):

pip install -U networkx matplotlib scikit-learn scipy pycorenlp

SpaCy

You need to install SpaCy. To do so, 3 solutions.

Solution 1: Installing Visual Studio Express 2015 (https://www.visualstudio.com/vs/visual-studio-express, free but takes 12 GB of space on the hard drive), then run:

pip install -U spacy
python -m spacy.en.download

Solution 2: Use Anaconda, in which case there is no need to install Visual Studio Express 2015:

conda config --add channels conda-forge
conda install spacy
python -m spacy.en.download
python -m spacy download en

Solution 3: Download from http://www.lfd.uci.edu/~gohlke/pythonlibs these precompiled Python packages (you may use a more recent version of the packages, but it should end with -cp35-cp35m-win_amd64.whl, which indicates they are compiled for Python 3.5 64-bit.):

  • cymem-1.31.2-cp35-cp35m-win_amd64.whl
  • murmurhash-0.26.4-cp35-cp35m-win_amd64.whl
  • preshed-1.0.0-cp35-cp35m-win_amd64.whl
  • thinc-6.5.2-cp35-cp35m-win_amd64.whl
  • spacy-1.8.2-cp35-cp35m-win_amd64.whl

Then, run from the command prompt:

pip install cymem-1.31.2-cp35-cp35m-win_amd64.whl
pip install murmurhash-0.26.4-cp35-cp35m-win_amd64.whl
pip install preshed-1.0.0-cp35-cp35m-win_amd64.whl
pip install thinc-6.5.2-cp35-cp35m-win_amd64.whl
pip install spacy-1.8.2-cp35-cp35m-win_amd64.whl
python -m spacy.en.download

Perl

You also need to install Perl (because the official CoNLL-2003 evaluation script is written in Perl): http://strawberryperl.com

Make sure the perl.exe binary is in your Path system environment variable:

BRAT (optional)

Installing BRAT is optional: it is only needed to easily create, change or view the annotations. BRAT does not run natively on Microsoft Windows, however it runs smoothly on Cygwin. After installing Cygwin, run Cygwin.bat (by default located on C:\cygwin64\ if you used the 64-bit installation for Cygwin). Then, in the terminal that just opened, run:

mkdir brat
cd brat
wget http://weaver.nlplab.org/~brat/releases/brat-v1.3_Crunchy_Frog.tar.gz
tar xzf brat-v1.3_Crunchy_Frog.tar.gz
cd brat-v1.3_Crunchy_Frog
./install.sh -u
python standalone.py

BRAT should now be accessible through the web browser at http://127.0.0.1:8001.

TensorBoard (optional)

The tensorboard.exe binary should also be in your Path system environment variable, if you plan to use TensorBoard (optional).

You can now download and run NeuroNER.