Design and implementation of an immune system simulator

Cellular automata based models have proven capable of providing several new insights into the dynamics of the immune system (IS) response. A qualitative picture of the IS behavior can be obtained with small-scale simulations. However, for a more detailed analysis and to further validate the models, large-scale simulations are required. To this purpose we present here a simulator (PARIMM) of the IS response which has been carefully designed and coded to allow such simulations (millions of cells with a very high degree of complexity). The code does not just resort to parallel processing to run faster. Data structures and I/O have been optimized as well to limit the (huge) memory and disk space requirements. The recent addition of the description of the T killer cellular mediated response allows the code to simulate both humoral and cellular immune reactions. All these features put PARIMM among the most complete simulators of the immune system developed up today. (C) 2001 Elsevier Science Ltd. All rights reserved.