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GPU-powered model analysis with PySB/cupSODA (2017)


Harris, LA, Nobile, MS, Pino, JC, Lubbock, ALR, Besozzi, D, Mauri, G, Cazzaniga, P, Lopez, CF (2017). GPU-powered model analysis with PySB/cupSODA. Bioinformatics, 33, 21:3492-3494.


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 high-dimensional 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 order-of-magnitude speedups relative to a CPU-based ordinary differential equation integrator.

Availability and implementation:

The PySB/cupSODA interface has been integrated into the PySB modeling framework (version 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manager such as pip. cupSODA source code and precompiled binaries (Linux, Mac OS/X, Windows) are available at (requires an Nvidia GPU; Additional information about PySB is available at

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Supplementary information:

Supplementary data are available at Bioinformatics online.

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