Cellular automata-based modeling program: synthetic immune system.

This article describes the functionality of a cellular automata-based immune system simulator, which we call SIS (synthetic immune system). SIS is based on descriptive cellular states and rules that define transitions between these states to model an entire immune system. Through the use of this program, an immunologist can test the validity of a proposed model by observing how it responds to self and non-self antigen. The output is then compared with the behavior of a real protective immune system, and the model can then be ruled as being adequate or inadequate. SIS-I, the first version of SIS written, has been modified through the years and is now available on our Web site: (http://www.cig.salk.edu/sis-I/sis.html). Although SIS-I has some flexibility, it has many hardwired values as well as a predefined keyword language for writing immune system rules. SIS-II was developed from SIS-I and allows the user to change more variables and to define keywords used within the program. Herein, we give an overview on how to use SIS-I and SIS-II, along with a future direction, SIS-III.