GPU-powered biochemical simulation

GPUs are massively multi-core accelerators designed for computer graphics that can be leveraged to distribute the calculations in scientific computing.

I worked on the acceleration of biochemical simulators, leveraging GPU’s cores to accelerate multiple simulations of a same model (“coarse-grained” acceleration) or to accelerate the simulation of a single massive model (“fine-grained” acceleration).


Coarse-grained simulators

cupSODA

cupSODA is a GPU-powered deterministic biochemical simulator for models based on mass-action kinetics, based on the LSODA integration algorithm.

More information about cupSODA is available on GITHUB.

PySB/cupSODA

PySB is a framework for building mathematical models of biochemical systems as Python programs. PySB is a powerful tool for rule-based modeling and it is now integrated with the GPU-powered deterministic biochemical simulator cupSODA.

Read the paper about PySB/cupSODA on Bioinformatics

cuTauLeaping

cuTauLeaping is a GPU-powered stochastic biochemical simulator based on Cao’s version of the tau leaping algorithm.

More information about cuTauLeaping is available on GITHUB.


Fine-grained simulators

LASSIE

LASSIE is a GPU-powered deterministic biochemical simulator for large-scale models based on mass-action kinetics.

More information about LASSIE is available on GITHUB.