1. Creating NOA (node attribute) files

2. What are Node Attributes? ● Nodes are the circles in your Cytoscape graph that can represent anything from organisms to cell phones. ● Node Attributes provide additional information about nodes. In a food web, node attributes can tell us which nodes are primary producers, which are primary consumers, etc. ● Node Attribute Files are text files with the “.noa” extension, containing node attribute information.

3. Making.noa files ● Click the Start button in the lower-left hand corner of your screen. ● Choose “Run...” ● Type “notepad” into the box and press Enter. ● Enter node attribute data as shown below: First line indicates name of attribute Subsequent lines indicate the value of the attribute for a given node.

4. Saving your.noa file ● Choose File/Save As... ● Give your file a name that matches the attribute name, and add a.noa extension. For example, role.noa ● Enclose the file name in double quotes before saving.

5. Load your.noa file into Cytoscape ● Assuming you still have Cytoscape open with your food web network showing, ● Choose File/Load/Node Attributes and type in your filename (in this case, role.noa).

6. Voilà! ● Two nodes changed color. Why? Because a predefined visual style was associated with the attribute “role” and the values “primary_producer” and “primary_consumer”. Later you will learn more about visual styles.

7. Additional Presets In addition to the “role” attribute, the attribute “diet” has been given a predefined visual style. You can create a file called diet.noa that looks like this (these examples are not necessarily factually correct): diet salmon = hervibore seals = carnivore herring = omnivore This visual style affects the shape of the nodes. Herbivores are triangles, omnivores are diamonds, and carnivores are squares.

8. Saving Your Project ● To get to where you are now, you had to do separate steps: first, load your network (sif) file, then your node attribute (noa) file. ● You can save your whole project to a single folder with one click—choose File/Save/Project (network=sif).... This will save all files associated with your project—.sif file,.noa files, and visual properties—to the directory of your choice. ● Later you can reload your project by choosing File/Load/Project....