Cytoscape

Cystoscape is an innovative piece of software capable of compiling visual networks of nodes and edges. During the internship, we worked on creating a visual network of the "culprits" and "victims" of ocean acidification, which was implemented as a part of the curriculum modules distributed to teachers.

Start by creating an Excel spreadsheet and writing relationships between components of the network. The relationships must have the same connection; in the example below, "impacts" is used as the connection. Other examples could be "bear eats salmon," "Donald likes coupons," or "interns eat icecream."

After you have completed your network, save the Excel spreadsheet as a sif file. To do this, designate the title of your network in between 2 quotes with .sif as the extension. For example, if you wanted to name your network Ocean Acidification, you would type in "Ocean Acidification.sif" in the File Name bar. Select "Text (tab delimited)" in the save as type bar.

Download Cytoscape by visiting http://www.cytoscape.org/ and following the instructions.

Import your network in Cytoscape by opening your .sif file. (File -> Import -> Network from Table (Text/MS Excel))

You can now manipulate the nodes and edges using your mouse. Hurray! Once you are satisfied with the layout, save it as a Cytoscape network by going to File -> Save As, and type in a title for your network. Important Note: Do not save the cytoscape network as a .sif file, and do not use quotes. Simply save it as a desired title under "All Files" for the File Type.