Home

Welcome to the cupSODA wiki.

cupSODA is a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm, LSODA. cupSODA can achieve a relevant speedup on GPUs with respect to equivalent executions of LSODA on the CPU.

Information about the command line arguments and the structure of the input files accepted by cupSODA can be found at the following address:

https://docs.google.com/document/d/1gPq-mYk-IP-bVmiMZewGPmTJ6nMCH8al1nNr7OaBsv4/edit?usp=sharing