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cyREST Examples for Python Users

Introduction

This is a guide for Python users who want to use Cytoscape via cyREST workflows in IPython Notebooks.

cyREST Documentation

Requirments

I assume you are a Python programmer. You should know how to use pip, IPython Notebook, etc. Also, these examples a lot of 3rd party libraries to demonstrate realistic data analysis and visualization workflows. This means you have to install all of your dependencies manually.

How to Use Example Notebooks

  1. Make sure your machine already has Python and related libraries, such as ipython, numpy, scipy, pandas, etc.
  2. Start Cytoscape (cyREST should be installed!)
  3. Clone the repository: git clone https://github.com/idekerlab/cy-rest-python
  4. Change directory: cd cy-rest-python
  5. Start IPython Notebook: ipython notebook
  6. Select index.ipynb to start the example

Using Docker Instead

If you don't want to install everything by yourself, you can use our Docker container instead.

Building Container in this directory

docker build -t idekerlab/cyrest-demo:1.0 .

Running Container

docker run -d -p 80:8888 -v $PWD:/notebooks -e "PASSWORD=cyrest" -e "USE_HTTP=1" idekerlab/cyrest-demo:1.0

and open the notebook with your web browser. Make sure youy are using correct IP address!

View Examples in GitHub

If you just want to see sample notebooks, you can access them from this index page.

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