Carlos Lopez
Faculty Member
Last active: 3/14/2018

GPU-powered model analysis with PySB/cupSODA.

Harris LA, Nobile MS, Pino JC, Lubbock ALR, Besozzi D, Mauri G, Cazzaniga P, Lopez CF
Bioinformatics. 2017 33 (21): 3492-3494

PMID: 28666314 · PMCID: PMC5860165 · DOI:10.1093/bioinformatics/btx420

Summary - 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 github.com/aresio/cupSODA (requires an Nvidia GPU; developer.nvidia.com/cuda-gpus). Additional information about PySB is available at pysb.org.

Contact - paolo.cazzaniga@unibg.it or c.lopez@vanderbilt.edu.

Supplementary information - Supplementary data are available at Bioinformatics online.

© The Author(s) 2017. Published by Oxford University Press.

MeSH Terms (5)

Computer Simulation Kinetics Models, Biological Software User-Computer Interface

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