Making a Network in Cytoscape Institute for Systems

Making a Network in Cytoscape Institute for Systems Biology & Bellevue School District

Step 1: Research your network http: //oceanlink. island. net/oinfo/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 3 = organism Column 1 = 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 Open up this page: http: //halo. systemsbiology. net/cytoscape/blank Then click on the “Click Here to Start” Link.

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