GPU-powered model analysis with PySB/cupSODA

Leonard A. Harris, Marco Nobile, James C. Pino, Alex L.R. Lubbock, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Carlos F. Lopez (Corresponding author)

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)3492–3494
Number of pages3
JournalBioinformatics
Volume33
Issue number21
DOIs
Publication statusPublished - 1 Nov 2017
Externally publishedYes

Keywords

  • Computer Simulation
  • Kinetics
  • Models, Biological
  • Software
  • User-Computer Interface

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