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FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks

Published version
Peer-reviewed

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Authors

Tangherloni, Andrea  ORCID logo  https://orcid.org/0000-0002-5856-4453
Capitoli, Giulia 

Abstract

Mathematical models of biochemical networks can largely facilitate the comprehension of the mechanisms at the basis of cellular processes, as well as the formulation of hypotheses that can be tested by means of targeted laboratory experiments. However, two issues might hamper the achievement of fruitful outcomes. On the one hand, detailed mechanistic models can involve hundreds or thousands of molecular species and their intermediate complexes, as well as hundreds or thousands of chemical reactions, a situation generally occurring in rule-based modeling. On the other hand, the computational analysis of a model typically requires the execution of a large number of simulations for its calibration, or to test the effect of perturbations. As a consequence, the computational capabilities of modern Central Processing Units can be easily overtaken, possibly making the modeling of biochemical networks a worthless or ineffective effort. To the aim of overcoming the limitations of the current state-of-the-art simulation approaches, we present in this paper FiCoS, a novel “black-box” deterministic simulator that effectively realizes both a fine-grained and a coarse-grained parallelization on Graphics Processing Units. In particular, FiCoS exploits two different integration methods, namely, the Dormand–Prince and the Radau IIA, to efficiently solve both non-stiff and stiff systems of coupled Ordinary Differential Equations. We tested the performance of FiCoS against different deterministic simulators, by considering models of increasing size and by running analyses with increasing computational demands. FiCoS was able to dramatically speedup the computations up to 855×, showing to be a promising solution for the simulation and analysis of large-scale models of complex biological processes.

Description

Keywords

Research Article, Biology and life sciences, Computer and information sciences, Physical sciences, Research and analysis methods, Ecology and environmental sciences

Journal Title

PLOS Computational Biology

Conference Name

Journal ISSN

1553-734X
1553-7358

Volume Title

17

Publisher

Public Library of Science