Dataset Information
GPU-powered model analysis with PySB/cupSODA.
Ontology highlight
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.
SUBMITTER: Harris LA
PROVIDER: S-EPMC5860165 | biostudies-literature | 2017 Nov
REPOSITORIES: biostudies-literature
Publications
GPU-powered model analysis with PySB/cupSODA.
Bioinformatics (Oxford, England) 20171101 21
<h4>Summary</h4>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-b ...[more]