Computers and software have proved to be invaluable tools when visualizing and analyzing complex networks. With many members (aka "nodes") in a network, interacting through many different types of relationships (aka "edges") the resultant data can be staggering. Through many collaborations, groups of individuals have worked to develop programs that allow us to make meaning of these relationships and to understand and predict the emergent properties that result when understanding complex networks. One such common and powerful software platform is Cytoscape. Cytoscape is an open source tool that allows scientists to visualize network interactions while integrating multiple data types. To bring this standard in current science to students, we have developed a cytoscape simulation that allows students to better understand the nature of network studies through a cell phone network example.
Follow these links to learn more about the Cell Phone simulation, or to directly use the Cell Phone Simulation or to use our template to create your own simulation. See our Ecological Networks Module Description or our Ecological Networks Coursework to learn more about the student activities that surround this simulation.
Teachers also search for the best ways to visualize information in order to help students better understand all topics. NetLogo is a proven, user-designed tool that helps students visualize many complex topics. In order to aid students in understanding the network surrounding Halobacterium's energy producing purple membrane pigment, bacteriorhodopsin, we have developed a NetLogo simulation depicting this dynamic molecular network. This Purple Membrane Network Model is explored in our Environmental Impact on Gene Networks Module, which is currently being field tested.