Making a network in cytoscape l.jpg
This presentation is the property of its rightful owner.
Sponsored Links
1 / 9

Making a Network in Cytoscape PowerPoint PPT Presentation


  • 180 Views
  • Uploaded on
  • Presentation posted in: General

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

Download Presentation

Making a Network in Cytoscape

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Making a network in cytoscape l.jpg

Making a Network in Cytoscape

Institute for Systems Biology & Bellevue School District


Step 1 research your network l.jpg

Step 1: Research your network

http://oceanlink.island.net/oinfo/foodweb/foodweb.html


Understanding the food web l.jpg

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.


Step 1 create a sif simple interaction format file l.jpg

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 l.jpg

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


Slide6 l.jpg

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


Step 3 load sif file into cytoscape l.jpg

File

Load

Interaction…

your SIF file

Step 3: load SIF file into Cytoscape


Cytoscape creates a network l.jpg

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 l.jpg

More info, bigger network


  • Login