Cytoscape Tutorial- Beginners Guide in Jupyter

Build beautiful graphical networks in Cytoscape! Cytoscape lets biologist, data scientists, and beginner programmers build and analyze graphical networks. You also can turn your graph in a website or computer code with just the click of a button!

Cytoscape is graphical software originally made by Trey Ideker’s lab. I created a new version of Cytoscape inside Jupyter io to make it easier for Biologists to build graphs and share their ideas with others. Jupyter is the most popular platform for data science, with it you can easily analyze your graphical network using python or R.

Introduction- 0:0
Cytoscape is useful to everyone who uses graphical networks, from biology to computer science to statistics. With graphs computational biologists can express complicated molecular pathways in a simple way. I built Cytoscape with the idea that non-programmers can create graphical networks which can then be shared everyone. These graphs can be turned into websites or saved into code. I built Cytoscape on top cytoscape.js which was made out of Cytoscape from Trey Ideker’s lab. My new Cytoscape is made inside of io to connect biologists with programmers. io has tons of bioinformatics software on it ready to use, like cytoscape, gene pattern notebook, and kallisto.

Make Graphs- 4:05
I show how to launch a python notebook with Cytoscape inside it. You add nodes and edges into you graph using just a few clicks. I change the size and colors of nodes and edges in Cytoscape to create the graph, Mr. Smiley. I should how you add data and labels to Cytoscape so that you can connect biological meaning to your graph. I show how to search through large networks.

Your Website- 9:34
We turn the graph we made into a website that is shared online with the world. We turn our network into an interactive html file. I introduce how you can use io online to share your work with others. We use io online to load our graph to Github were it automatically turned into a website. You can use io online to update you applications, share you work, and communicate with your lab.

Code Graphs- 15:04
Cytoscape is made inside of Jupyter which makes doing data analysis on your graph easy. You can launch Cytoscape inside of any jupyter notebook. You can then load any Cytoscape network as a pandas data frame. Pandas then lets you easily analyze your data or convert it to a CSV file for data analysis in R.

Conclusion- 19:11
I explain how you can install io by watching this video:    • io- Install Python Java C++ R on Mac, Wind...   . I made io so that total beginners have everything they need for bioinformatics coding on any device (ios, windows, chrome). In a later video I explain the source code for Cytoscape. If your a biologist or programmer and you do something cool with Cytoscape let me know!

Awesome Links to learn more:
Install io
   • io- Install Python Java C++ R on Mac, Wind...  
Cytoscape.js
http://js.cytoscape.org/
Cytoscape Site
https://cytoscape.org/
Trey Ideker’s lab
https://medschool.ucsd.edu/som/medici...

What is Jupyter? What is io?
Jupyter is a new operating system has become the most popular tool in data science. io is a new version of jupyter that is perfect for beginners wanting learn how to code, because it’s easy to install and gives you all the tools you need. io also lets you program on any device! (microsoft, mac, android, ios) This is because io is a website that runs on google cloud compute engine. I also show how you can build fast jupyter applications using io online.