Making%20a%20Network%20in%20Cytoscape

1
Making a Network in Cytoscape
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
  Eating/being Eaten by another organism
• 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 2
Create a 3 column file in Excel
5
Step 2, continued

• Save as a Text (Tab Delimited) file
• Write in .sif at the end of the file name, and
  include the entire file name in quotation marks
• For example, salmonfoodweb.sif

6
Start Up a Blank Cytoscape
http//halo.systemsbiology.net/cytoscape/cellphone
7
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