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A Lock Free Approach To Parallelize The Cellular Potts Model: Application To Ductal Carcinoma In Situ.

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Bibliographic Details
Title: A Lock Free Approach To Parallelize The Cellular Potts Model: Application To Ductal Carcinoma In Situ.
Authors: Tomeu, Antonio J., Salguero, Alberto G.
Source: Journal of Integrative Bioinformatics; 2020, Vol. 17 Issue 1, p1-11, 11p
Subject Terms: COMPUTATIONAL biology, ADENOCARCINOMA, COMPUTER software, MULTICORE processors, COMPUTER simulation
Abstract: In the field of computational biology, in order to simulate multiscale biological systems, the Cellular Potts Model (CPM) has been used, which determines the actions that simulated cells can perform by determining a hamiltonian of energy that takes into account the influence that neighboring cells exert, under a wide range of parameters. There are some proposals in the literature that parallelize the CPM; in all cases, either lockbased techniques or other techniques that require large amounts of information to be disseminated among parallel tasks are used to preserve data coherence. In both cases, computational performance is limited. This work proposes an alternative approach for the parallelization of the model that uses transactional memory to maintain the coherence of the information. A Java implementation has been applied to the simulation of the ductal adenocarcinoma of breast in situ (DCIS). Times and speedups of the simulated execution of the model on the cluster of our university are analyzed. The results show a good speedup. [ABSTRACT FROM AUTHOR]
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Database: Complementary Index
Description
Abstract:In the field of computational biology, in order to simulate multiscale biological systems, the Cellular Potts Model (CPM) has been used, which determines the actions that simulated cells can perform by determining a hamiltonian of energy that takes into account the influence that neighboring cells exert, under a wide range of parameters. There are some proposals in the literature that parallelize the CPM; in all cases, either lockbased techniques or other techniques that require large amounts of information to be disseminated among parallel tasks are used to preserve data coherence. In both cases, computational performance is limited. This work proposes an alternative approach for the parallelization of the model that uses transactional memory to maintain the coherence of the information. A Java implementation has been applied to the simulation of the ductal adenocarcinoma of breast in situ (DCIS). Times and speedups of the simulated execution of the model on the cluster of our university are analyzed. The results show a good speedup. [ABSTRACT FROM AUTHOR]
ISSN:16134516
DOI:10.1515/jib-2019-0070