Tomeu Antonio J, Salguero Alberto G
University of Cadiz, Computer Science, Escuela Superior de Ingeniería, Campus of Puerto RealPuerto Real, Spain.
University of Cadiz, Faculty of Engineering, Department of Computer Science, Puerto Real, Spain.
J Integr Bioinform. 2020 Apr 7;17(1):20190070. doi: 10.1515/jib-2019-0070.
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 lock-based 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.
在计算生物学领域，为了模拟多尺度生物系统，人们使用了细胞Potts模型（CPM），该模型通过确定一个能量哈密顿量来决定模拟细胞可以执行的动作，该能量哈密顿量考虑了在广泛参数范围内相邻细胞施加的影响。文献中有一些将CPM并行化的提议；在所有情况下，要么使用基于锁的技术，要么使用需要在并行任务之间传播大量信息的其他技术来保持数据一致性。在这两种情况下，计算性能都受到限制。这项工作提出了一种用于该模型并行化的替代方法，该方法使用事务内存来维护信息的一致性。一个Java实现已应用于乳腺原位导管腺癌（DCIS）的模拟。分析了该模型在我校集群上模拟执行的时间和加速比。结果显示出良好的加速比。
