GPU-powered Simulation Methodologies for Biological Systems
نویسندگان
چکیده
منابع مشابه
GPU-powered Simulation Methodologies for Biological Systems
In the last decades, the study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods, thanks to the convergence of the so-called high-throughput era with the easy access to high performance computing resources. This combination gave rise to the development of new methodologies, able to tackle the complexity of biological sys...
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Copyright: 2014 The PLOS ONE Staff. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Figure 13. Performance comparison of CPU tau-leaping and cuTauLeaping for a PSA of the Ras/cAMP/PKA model. Running times of c...
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Tau-leaping is a stochastic simulation algorithm that efficiently reconstructs the temporal evolution of biological systems, modeled according to the stochastic formulation of chemical kinetics. The analysis of dynamical properties of these systems in physiological and perturbed conditions usually requires the execution of a large number of simulations, leading to high computational costs. Sinc...
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Computer-interpretable representations of system structure and behavior are at the center of designing today’s complex systems. Engineers create and review such representations using graphical modeling languages that support specification, analysis, design, verification and validation of systems that include hardware, software, data, personnel, procedures, and facilities, such as the Systems Mo...
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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...
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ژورنال
عنوان ژورنال: Electronic Proceedings in Theoretical Computer Science
سال: 2013
ISSN: 2075-2180
DOI: 10.4204/eptcs.130.14