title: Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization.
abstract: The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.
authors.affiliation: Dipartimento di Scienze Umane e Sociali, Università degli Studi di Bergamo, 24129 Bergamo, Italy ; SYSBIO Centre for Systems Biology, 20126 Milano, Italy ; Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", Consiglio Nazionale delle Ricerche, 00185 Roma, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Cazzaniga
authors.affiliation: SYSBIO Centre for Systems Biology, 20126 Milano, Italy ; Università degli Studi di Milano-Bicocca, Dipartimento di Informatica, Sistemistica e Comunicazione, 20126 Milano, Italy.
authors.forename: Marco S
authors.initials: MS
authors.lastname: Nobile
authors.affiliation: SYSBIO Centre for Systems Biology, 20126 Milano, Italy ; Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", Consiglio Nazionale delle Ricerche, 00185 Roma, Italy ; Università degli Studi di Milano, Dipartimento di Informatica, 20135 Milano, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Besozzi
authors.affiliation: Università degli Studi di Milano-Bicocca, Dipartimento di Informatica, Sistemistica e Comunicazione, 20126 Milano, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Bellini
authors.affiliation: SYSBIO Centre for Systems Biology, 20126 Milano, Italy ; Università degli Studi di Milano-Bicocca, Dipartimento di Informatica, Sistemistica e Comunicazione, 20126 Milano, Italy.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Mauri
mesh_terms: D000465:Algorithms; D001777:Blood Coagulation; D019295:Computational Biology; D003196:Computer Graphics; D003198:Computer Simulation; D003205:Computing Methodologies; D006801:Humans; D008954:Models, Biological; D012984:Software; D049490:Systems Biology