Investigating the speedup of systems biology simulation using the SZTAKI Desktop Grid

Abstract

Systems biology studies the complex interactions of biological and biochemical systems rather than their individual molecular components. System biology simulations can be embarrassingly parallel jobs that have no dependency among individual simulation instances, and thus lend themselves to parallel execution over distributed resources to reduce their overall execution time. One example of such distributed resources is a Desktop Grid for Volunteer Computing that aims to use vast numbers of computers to support scientific applications. The SZTAKI Desktop Grid (SZDG) uses a modified form of the volunteer computing software BOINC to implement an institution-wide Desktop Grid. This paper reports on experiences of porting the SIMAP systems biology ODE simulator to SZDG. A case study using a simulation of the mammalian ErbB signaling pathway reports on significant speedup.