Elementary mode analysis is a useful metabolic pathway analysis tool in understanding and analyzing cellular metabolism, since elementary modes can represent metabolic pathways with unique and minimal sets of enzyme-catalyzed reactions of a metabolic network under steady state conditions. However, computation of the elementary modes of a genome- scale metabolic network with 100-1000 reactions is very expensive and sometimes not feasible with the commonly used serial Nullspace Algorithm. In this work, we develop a distributed memory parallelization of the Nullspace Algorithm to handle efficiently the computation of the elementary modes of a large metabolic network. We give an implementation in C++ language with the support of MPI library functions for the parallel communication. Our proposed algorithm is accompanied with an analysis of the complexity and identification of major bottlenecks during computation of all possible pathways of a large metabolic network. The algorithm includes methods to achieve load balancing among the compute-nodes and specific communication patterns to reduce the communication overhead and improve efficiency.

中文翻译：

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用于计算代谢途径的零空间算法的并行化。

基本模式分析是理解和分析细胞代谢的有用代谢途径分析工具，因为基本模式可以代表代谢途径，在稳态条件下，代谢网络具有独特和最小的酶催化反应集。然而，计算具有 100-1000 次反应的基因组规模代谢网络的基本模式非常昂贵，有时使用常用的串行空空间算法是不可行的。在这项工作中，我们开发了 Nullspace 算法的分布式内存并行化，以有效处理大型代谢网络的基本模式的计算。我们给出了一个支持并行通信的 MPI 库函数的 C++ 语言实现。我们提出的算法伴随着对大型代谢网络所有可能途径的计算过程中主要瓶颈的复杂性和识别的分析。该算法包括在计算节点之间实现负载平衡的方法和特定的通信模式，以减少通信开销并提高效率。