creating basic workflows as jupyter notebooks to use cytoscape programmatically

Creating basic workflows as Jupyter Notebooks to use

Cytoscape programmatically.

@St_Hakky

Project Goal• Target• Someone who want to use Cytoscape programmatically

by cyREST(py2cytoscape, RCy3).

• Project Goal• Provide the stable environment for network analysis

with cyREST and python or R by using docker container.

• Provide reusable and scalable workflows as Jupyter Notebook with cyREST(py2cytoscape/RCy3).

By this project, you can…• Create your network analysis environment quickly

by docker without no dependency-hell• Usually, the environment is so complicated and you

spend a lot of time and it will cause dependency-hell.

By this project, you can…• Automate your typical or usual tasks with cyREST• Applying different layouts to 100 networks by hand is

possible, but ridiculous• There are Python and R wrapper for cyREST :

py2cytoscape and RCy3.• The workflow include import data, apply layout, add

annotation from database, etc...

By this project, you can…• Use reusable and scalable workflows as Jupyter

notebook and make your code in Jupyter notebook.

Overview of this project

1. Build Environment for network analysis

2. Use Cytoscape programatically

3. Execute reusable workflows and your code in jupyter noteobok

Demo

You can build your enviroment by docker.• When you setup your docker environment, the only

thing to do is typing following code.

docker run -d -p 8888:8888 -v /Your/work/space/path:/home/jovyan/work cyrest/examples

• When you type it, you can get environment.

The contents of environment by docker• For Python Users

• Pytho 2.x and 3.x• graph-tools• igraph• networkx• pandas• numpy• scipy• jupyter notebook• py2cytoscape

• For R Users• Bioconductor• Jupyter Notebook• Igraph• RCy3

The more detail and docker Image here.URL : https://github.com/idekerlab/cyrest-examples

You can use following packages by creating environment with docker

The contents of Workflows In this project, I prepare many reusable and useful workflows.

【 Contents】• Import data• Network Analysis• Layout• Style• Export• Other useful methods• Realistic workflows

Future plan• Complete Cookbook• Make Py2cytoscape documentation• Add Realistic workflow for bioinfomatician• Report some bugs in RCy3 and py2cytoscape at

github repogitory and make some useful function for RCy3 and py2cytoscape users.