In silico simulation of biological network dynamics
In silico simulation of biological network dynamics
复制标题
DOI：
10.1038/nbt991
复制
发表时间：
2004-08-01
影响因子：
46.9
通讯作者：
Eisenberg, D
中科院分区：
文献类型：
--
作者：
Salwinski, L;Eisenberg, D
生物网络的真实模拟需要随机模拟方法，因为每个细胞的分子数量很少。在传统的基于微处理器的计算机上进行随机模拟的高计算成本源于微处理器程序执行的顺序步骤与生物化学网络中信息流的高度并行性之间的内在差异。这种差异是减少与现场可编程门阵列（FPGA）为基础的方法在这里提出。fpga的并行架构可以模拟生物网络的基本反应步骤，其模拟速率至少比目前可用的微处理器高一个数量级。
Realistic simulation of biological networks requires stochastic simulation approaches because of the small numbers of molecules per cell. The high computational cost of stochastic simulation on conventional microprocessor-based computers arises from the intrinsic disparity between the sequential steps executed by a microprocessor program and the highly parallel nature of information flow within biochemical networks. This disparity is reduced with the Field Programmable Gate Array (FPGA)-based approach presented here. The parallel architecture of FPGAs, which can simulate the basic reaction steps of biological networks, attains simulation rates at least an order of magnitude greater than currently available microprocessors.