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- Title
GPU-powered model analysis with PySB/cupSODA.
- Authors
Harris, Leonard A.; Nobile, Marco S.; Pino, James C.; Lubbock, Alexander L. R.; Besozzi, Daniela; Mauri, Giancarlo; Cazzaniga, Paolo; Lopez, Carlos F.
- Abstract
A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over highdimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework. For three example models of varying size, we show that for large numbers of simulations PySB/cupSODA achieves orderof- magnitude speedups relative to a CPU-based ordinary differential equation integrator.
- Subjects
GRAPHICS processing units; SIMULATION methods &; models; COMPUTER software; ORDINARY differential equations; INTEGRATORS
- Publication
Bioinformatics, 2017, Vol 33, Issue 21, p3492
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btx420