A biological optimization problem on the Grid

Vaccine and drug discovery is a lengthy process. Mathematical-computational models can speed-up the process. In cancer immunology the Triplex vaccine [Pappalardo et al.(2005)] prevented mammary carcinoma formation in HER-2/Neu mouse models using a Chronic Schedule, but it is not known if this schedule is minimal. The use of the SimTriplex model and Genetic Algorithms produced a minimal vaccination schedule capable of guarantee in silico survival [Pappalardo et al.(2005)] requiring an HPC infrastructure for several days. In this paper we show a novel optimal protocol search algorithm based on Simulated Annealing (SA) capable to greatly reduce the computational effort. The COMETA grid infrastructure has been used for protocol search and validation.