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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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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

  • 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.


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:


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


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


File

Load

Interaction…

your SIF file

Step 3: load SIF file into Cytoscape


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.


More info, bigger network


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