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

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Presentation transcript:

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

Step 1: Research your network

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 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