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

2. Step 1: Research your network http://oceanlink.island.net/oinfo/foodweb/foodweb.html

3. 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.

4. 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)

5. 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

6. 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:

7. Step 3: load SIF file into Cytoscape File Load Interaction… your SIF file

8. 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.

9. More info, bigger network