by Kozo Nishida, Barry Demchak, Alexander Pico
pywikipathways 0.0.2
py4cytoscape 0.0.10
WikiPathways is a well-known repository for biological pathways that provides unique tools to the research community for content creation, editing and utilization [@Pico2008].
Python is a powerful programming language and environment for statistical and exploratory data analysis.
pywikipathways leverages the WikiPathways API to communicate between Python and WikiPathways, allowing any pathway to be queried, interrogated and downloaded in both data and image formats. Queries are typically performed based on “Xrefs”, standardized identifiers for genes, proteins and metabolites. Once you can identified a pathway, you can use the WPID (WikiPathways identifier) to make additional queries.
py4cytoscape leverages the CyREST API to provide a number of functions related to network visualization and analysis.
In addition to this pywikipathways package, you’ll also need to install cytoscape and py4cytoscape:
!pip install pywikipathways
The whole point of py4cytoscape is to connect with Cytoscape. You will need to install and launch Cytoscape:
- Download the latest Cytoscape from http://www.cytoscape.org/download.php
- Complete installation wizard
- Launch Cytoscape
- Install FileTransfer App (Follow here to do it.)
NOTE: To run this notebook, you must manually start Cytoscape first – don’t proceed until you have started Cytoscape.
If you’re using a remote Jupyter Notebook environment such as Google Colab, run the cell below. (If you’re running a local Jupyter Notebook server on the desktop machine same with Cytoscape, you don’t need to do that.)
_PY4CYTOSCAPE = 'git+https://github.com/cytoscape/py4cytoscape@0.0.10'
import requests
exec(requests.get("https://raw.githubusercontent.com/cytoscape/jupyter-bridge/master/client/p4c_init.py").text)
IPython.display.Javascript(_PY4CYTOSCAPE_BROWSER_CLIENT_JS) # Start browser client
First, confirm that you have everything installed and running: