Making a Network in Cytoscape

Institute for Systems Biology & Bellevue School District

Step 1: Research your network

http://oceanlink.island.net/oinfo/foodweb/foodweb.html

Understanding The Food Web• One type of interaction in this food web:

organisms eating other organisms

• This web page tells me that:– Salmon eats herring– Salmon is eaten by seals, killer whales, sea

birds, scavengers, and decomposers– The energy flow in a food web moves from

organisms which are eaten towards organisms which eat them.

Step 1: Create a SIF (Simple Interaction Format) File

Create a 3 column file in Excel:

Column 1 = organism

Column 3 = organism

Column 2 = interaction (is eaten by)

Save your SIF file• File Name: Write in .sif at the end of the file name, and

include the entire file name in quotation marks:For example: “myfoodweb.sif”

• Save as type: Text (Tab Delimited)

File name

Save as type

Step 2:Open a Blank Cytoscape

http://halo.systemsbiology.net/cytoscape/blank

Then click on the “Click Here to Start” Link.

Open up this page:

Step 3: load SIF file into Cytoscape

File Load Interaction…

your SIF file

Cytoscape creates

a network:

•This type of layout is “Organic”

•See “Layout” menu to explore different layouts (choose a layout, then press Control-L).

•See “Visualization” menu to explore visual aspects of network.

More info, bigger network