title: On designing multicore-aware simulators for systems biology endowed with OnLine statistics.
abstract: The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the FastFlow parallel programming framework, are shown on a simulation tool to perform the modeling, the tuning, and the sensitivity analysis of stochastic biological models. A stochastic simulation needs thousands of independent simulation trajectories turning into big data that should be analysed by statistic and data mining tools. In the considered approach the two stages are pipelined in such a way that the simulation stage streams out the partial results of all simulation trajectories to the analysis stage that immediately produces a partial result. The simulation-analysis workflow is validated for performance and effectiveness of the online analysis in capturing biological systems behavior on a multicore platform and representative proof-of-concept biological systems. The exploited methodologies include pattern-based parallel programming and data streaming that provide key features to the software designers such as performance portability and efficient in-memory (big) data management and movement. Two paradigmatic classes of biological systems exhibiting multistable and oscillatory behavior are used as a testbed.
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy.
authors: Marco
authors: 0000-0001-8788-0829
authors: M
authors: Aldinucci
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy ; Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy.
authors: Cristina
authors: C
authors: Calcagno
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy.
authors: Mario
authors: M
authors: Coppo
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy.
authors: Ferruccio
authors: 0000-0001-8109-1706
authors: F
authors: Damiani
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy.
authors: Maurizio
authors: 0000-0001-6500-7607
authors: M
authors: Drocco
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy.
authors: Eva
authors: 0000-0002-5574-2787
authors: E
authors: Sciacca
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy.
authors: Salvatore
authors: 0000-0002-1541-0083
authors: S
authors: Spinella
authors: Department of Computer Science, University of Pisa, 56127 Pisa, Italy.
authors: Massimo
authors: 0000-0001-6323-3459
authors: M
authors: Torquati
authors: Department of Computer Science, University of Torino, 10149 Torino, Italy.
authors: Angelo
authors: 0000-0002-0049-4237
authors: A
authors: Troina
mesh_terms: D010582:Bacteriophage lambda / Q000502:physiology; D003198:Computer Simulation; D003600:Cytosol / Q000378:metabolism; D005656:Fungal Proteins / Q000378:metabolism; D008954:Models, Biological; D009491:Neurospora / Q000378:metabolism; D009862:Online Systems / Q000295:instrumentation*; D012985:Software Design; D013223:Statistics as Topic; D049490:Systems Biology / Q000295:instrumentation*; D014584:User-Computer Interface
chemical_list: D005656:Fungal Proteins