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Making a Network in Cytoscape

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

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Making a Network in Cytoscape

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  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 • Onetype 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. Column 3 = organism Column 1 = organism Column 2 = interaction (is eaten by) Step 1: Create a SIF (Simple Interaction Format) File Create a 3 column file in Excel:

  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. Open up this page: Then click on the “Click Here to Start” Link. Step 2: Open a Blank Cytoscape http://halo.systemsbiology.net/cytoscape/blank

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

  8. Cytoscape createsa 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

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