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Bioinformatics. 2017 Nov 1;33(21):3492-3494. doi: 10.1093/bioinformatics/btx420.

GPU-powered model analysis with PySB/cupSODA.

Author information

1
Department of Cancer Biology.
2
Quantitative Systems Biology Center, Vanderbilt University, Nashville, TN 37232, USA.
3
Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.
4
SYSBIO.IT Centre of Systems Biology, Milan, Italy.
5
Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN 37232, USA.
6
Department of Human and Social Sciences, University of Bergamo, Bergamo, Italy.

Abstract

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.

PMID:
28666314
PMCID:
PMC5860165
DOI:
10.1093/bioinformatics/btx420
[Indexed for MEDLINE]
Free PMC Article

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